<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hey Mark..<DIV>I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. </DIV><DIV>I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working. But when I tried to do the MD run after a small minimization of protein, I got an error message after the execution of grompp. The execution asked for the -n option which indicates for the index file. 1) I don't know why it asked for?</DIV><DIV>2) If it ask for is there any way to solv this problem. Actually i tried using that also. But the error stayed back. </DIV><DIV>I am also pasting the error after the grompp. Somehow this could not prepare the input file for the MD run. </DIV><DIV>3) third question is: I am wondering whether i can start my run just after the execution of pdb2gmx. Any ways 1) the system is in vacuum and second while running it for quite long, minimization of energy will automatically take place.</DIV><DIV>******************************************************************************</DIV><DIV>ERROR:</DIV><DIV>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#</DIV><DIV>checking input for internal consistency...</DIV><DIV>Generated 279 of the 1225 non-bonded parameter combinations</DIV><DIV>Excluding 3 bonded neighbours for Protein 1</DIV><DIV>processing coordinates...</DIV><DIV>double-checking input for internal consistency...</DIV><DIV>Velocities were taken from a Maxwell distribution at 300 K</DIV><DIV>renumbering atomtypes...</DIV><DIV>converting bonded parameters...</DIV><DIV>Walking down the molecule graph to make shake-blocks</DIV><DIV>initialising group options...</DIV><DIV>processing index file...</DIV><DIV>-------------------------------------------------------</DIV><DIV>Program grompp, VERSION 3.3</DIV><DIV>Source code file: readir.c, line: 775</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Fatal error:</DIV><DIV>Group sol not found in indexfile.</DIV><DIV>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.</DIV><DIV>In that case use the '-n' option.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>*********************************************************</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>#!/bin/csh</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV># this is the demo molecule</DIV><DIV>setenv MOL ilepep</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>####################</DIV><DIV>### INTRODUCTION ###</DIV><DIV>####################</DIV><DIV>clear </DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>Welcome to the GROMACS demo.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>This is a script that takes about 10 min to run.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>In this demo we will demonstrate how to simulate Molecular</DIV><DIV>Dynamics (MD) using the GROMACS software package.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The demo will perform a complete molecular dynamics (MD) simulation</DIV><DIV>of a small peptide in water. The only input file we need to do this</DIV><DIV>is a pdb file of a small peptide.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If you have any problems or remarks with respect to this demonstration,</DIV><DIV>please mail to: <A href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</A> , or check the resources on</DIV><DIV>our website <A href="http://www.gromacs.org">http://www.gromacs.org</A> .</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>#########################</DIV><DIV>### CHECK ENVIRONMENT ###</DIV><DIV>#########################</DIV><DIV>clear </DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>Before we you can actually start the GROMACS demo, the programs</DIV><DIV>must be present in your PATH. This might already be the case if</DIV><DIV>they are linked to /usr/local/bin. If not, follow the instructions</DIV><DIV>in the getting started section. If GROMACS is not installed </DIV><DIV>properly on your computer, contact your system manager.</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>###############</DIV><DIV>### PDB2GMX ###</DIV><DIV>###############</DIV><DIV>clear</DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>Before we can start any simulation we need a molecular toplogy</DIV><DIV>file. This topology file ( .top extension ) is generated by the</DIV><DIV>program pdb2gmx. The only input file of the pdb2gmx program is the pdb</DIV><DIV>file of our peptide ( .pdb extension ). </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Because most pdb files do not contain all hydrogen atoms, the pdb2gmx</DIV><DIV>program will also add them to our peptide. The output file which</DIV><DIV>contains the structure of the peptide when hydrogen atoms are added is a</DIV><DIV>gromos structure file ( .gro extension ) </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>echo "You seem to have the DISPLAY variable is set, so we will"</DIV><DIV> echo "pop up a window with the output of the pdb2gmx program" </DIV><DIV>endif</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "Starting pdb2gmx"</DIV><DIV>if ( $?DISPLAY ) then </DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>xterm -title /nmr_apps_DarwinPPC/gromacs/bin/pdb2gmx -sb -e tail +0f output.pdb2gmx &</DIV><DIV>endif</DIV><DIV>echo 1 | /nmr_apps_DarwinPPC/gromacs/bin/pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx</DIV><DIV>echo "pdb2gmx finished"</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>##############</DIV><DIV>### GROMPP ###</DIV><DIV>##############</DIV><DIV>clear</DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>In principle we can start a Molecular Dynamics simulation now. However</DIV><DIV>it is not very wise to do so, because our system is full of close</DIV><DIV>contacts. These close contacts are mainly a result of the genbox</DIV><DIV>program. The added solvent might have some close contacts with the</DIV><DIV>peptide resulting in very high repulsive energies. If we would start a</DIV><DIV>Molecular Dynamics (MD) simulation without energy minimisation the</DIV><DIV>system would not be stable because of these high energies.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The standard procedure to remove these close contacts is</DIV><DIV>Energy Minimisation (EM). Energy minimisation slightly changes the</DIV><DIV>coordinates of our system to remove high energies from our system. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Before we can start the Energy Minimisation we have to preprocess all</DIV><DIV>the input files with the GROMACS preprocessor named grompp. grompp</DIV><DIV>preprocesses the topology file (.top), the structure file (.gro) and a</DIV><DIV>parameter file (.mdp) resulting in a binary topology file (.tpr</DIV><DIV>extension). This binary topology file contains all information for a </DIV><DIV>simulation (in this case an energy minimisation).</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>echo "The output of the grompp program should appear" </DIV><DIV> echo "in a separate xterm window"</DIV><DIV>endif</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo generating energy minimisation parameter file...</DIV><DIV>cat > em.mdp << _EOF_</DIV><DIV>title = ${MOL}</DIV><DIV>cpp = /usr/bin/cpp</DIV><DIV>define <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = -DFLEXIBLE</DIV><DIV>integrator = steep</DIV><DIV>nsteps = 200</DIV><DIV>emtol = 100</DIV><DIV>emstep = 0.01</DIV><DIV>nstcgsteep = 1000</DIV><DIV>nstxout = 0</DIV><DIV>nstvout = 0</DIV><DIV>nstfout = 0</DIV><DIV>nstlog = 100</DIV><DIV>nstenergy = 10</DIV><DIV>nstxtcout = 0</DIV><DIV>xtc-precision = 1000</DIV><DIV>xtc_grps = Protein</DIV><DIV>energygrps = Protein </DIV><DIV>nstlist = 0</DIV><DIV>ns_type = simple</DIV><DIV>pbc = no</DIV><DIV>rlist = 0</DIV><DIV>coulombtype = Cut-off</DIV><DIV>rcoulomb = 0</DIV><DIV>epsilon_r = 1</DIV><DIV>vdw-type = Cut-off</DIV><DIV>rvdw = 0</DIV><DIV>constraints = all-bonds</DIV><DIV>constraint-algorithm = Lincs</DIV><DIV>unconstrained-start = no</DIV><DIV>Shake-SOR = no</DIV><DIV>shake-tol = 1e-04</DIV><DIV>lincs-order = 4</DIV><DIV>lincs-iter = 4</DIV><DIV>lincs-warnangle = 30</DIV><DIV>morse = no</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "Starting grompp..."</DIV><DIV>if ( $?DISPLAY ) then </DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>xterm -title /nmr_apps_DarwinPPC/gromacs/bin/grompp -sb -e tail +0f output.grompp_em &</DIV><DIV>endif</DIV><DIV>/nmr_apps_DarwinPPC/gromacs/bin/grompp -f em -c ${MOL} -p ${MOL} -o ${MOL}_em >& ! output.grompp_em</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "grompp finished"</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>################</DIV><DIV>### MDRUN EM ###</DIV><DIV>################</DIV><DIV>clear</DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>Now the binary topology file is generated, we can start the energy</DIV><DIV>minimisation (EM). The program which performs the EM is called</DIV><DIV>mdrun. In fact all simulations are performed by the same program:</DIV><DIV>mdrun. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>As the Energy Minimisation is running, watch the output of the</DIV><DIV>program. The first number ( from left to right ) is the number of the</DIV><DIV>iteration step. The second number is the step size, which gives an</DIV><DIV>indication of the change in the system. The third number is the</DIV><DIV>potential energy of the system. This number starts at a high value and</DIV><DIV>rapidly drops down, and converges, to a large negative value. </DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>echo "The output of the mdrun program should appear"</DIV><DIV> echo "in a separate xterm window"</DIV><DIV>endif</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "starting energy minimisation mdrun..."</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then </DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>xterm -title /nmr_apps_DarwinPPC/gromacs/bin/mdrun -sb -e tail +0f output.mdrun_em &</DIV><DIV>endif</DIV><DIV>/nmr_apps_DarwinPPC/gromacs/bin/mdrun -nice 0 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4md -v >& ! output.mdrun_em </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "mdrun finished"</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>#################</DIV><DIV>### GROMPP MD ###</DIV><DIV>#################</DIV><DIV>clear</DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>Now our complete system is finally ready for the actual Molecular</DIV><DIV>Dynamics simulation. We start again by preprocessing the input files</DIV><DIV>by the grompp program to generate the binary topology file (.tpb/.tpr</DIV><DIV>extension).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>echo "The output of the grompp program should appear" </DIV><DIV> echo "in a separate xterm window"</DIV><DIV>endif</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "generating parameter file..."</DIV><DIV>cat > md.mdp << _EOF_</DIV><DIV>title = ${MOL} MD</DIV><DIV>cpp = /usr/bin/cpp</DIV><DIV>define <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = -DFLEXIBLE</DIV><DIV>constraints = all-bonds</DIV><DIV>integrator = md</DIV><DIV>dt = 0.002<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>; ps !</DIV><DIV>nsteps = 1000<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>; total 2 ps.</DIV><DIV>nstcomm = 1</DIV><DIV>nstxout = 500</DIV><DIV>nstvout = 500</DIV><DIV>nstfout = 0</DIV><DIV>nstlog <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = 500<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN></DIV><DIV>nstlist = 10</DIV><DIV>nstenergy<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = 125</DIV><DIV>ns_type = simple</DIV><DIV>comm_mode <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = ANGULAR</DIV><DIV>xtc_precision = 1000</DIV><DIV>xtc_grps = Protein</DIV><DIV>energygrps = Protein</DIV><DIV>rlist = 0</DIV><DIV>rcoulomb = Cut-off</DIV><DIV>rvdw = Cut-off</DIV><DIV>epsilon_r = 1.0</DIV><DIV>; Berendsen temperature coupling is on in two groups</DIV><DIV>Tcoupl = berendsen</DIV><DIV>tau_t = 0.1<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> 0.1</DIV><DIV>tc-grps<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = protein<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> sol</DIV><DIV>ref_t = 300<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> 300</DIV><DIV>;Periodic Boundary conditions</DIV><DIV>pbc <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> = No</DIV><DIV>; Pressure coupling is not on</DIV><DIV>Pcoupl = No</DIV><DIV>tau_p = 0.5</DIV><DIV>compressibility = 4.5e-5</DIV><DIV>ref_p = 1.0</DIV><DIV>; Generate velocites is on at 300 K.</DIV><DIV>gen_vel = yes</DIV><DIV>gen_temp = 300.0</DIV><DIV>gen_seed = 173529</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "Starting grompp..."</DIV><DIV>if ( $?DISPLAY ) then </DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>xterm -title /nmr_apps_DarwinPPC/gromacs/bin/grompp -sb -e tail +0f output.grompp_md &</DIV><DIV>endif</DIV><DIV>/nmr_apps_DarwinPPC/gromacs/bin/grompp -n -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "grompp finished"</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>################</DIV><DIV>### MDRUN MD ###</DIV><DIV>################</DIV><DIV>clear</DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>Now we can start the MD simualtion. Watch the number of steps</DIV><DIV>increasing ( the total number of steps is 5000, for 10 ps ).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>echo "The output of the mdrun program should appear" </DIV><DIV> echo "in a separate xterm window"</DIV><DIV>endif</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "starting mdrun..."</DIV><DIV>if ( $?DISPLAY ) then </DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>xterm -title /nmr_apps_DarwinPPC/gromacs/bin/mdrun -sb -e tail +0f output.mdrun_md &</DIV><DIV>endif</DIV><DIV>/nmr_apps_DarwinPPC/gromacs/bin/mdrun -nice 0 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>echo "mdrun finished"</DIV><DIV>echo -n "Press <enter>"</DIV><DIV>set ans = $<</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>############</DIV><DIV>### NGMX ###</DIV><DIV>############</DIV><DIV>clear</DIV><DIV>cat << _EOF_</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>We are finished simulating, and we are going to view the calculated</DIV><DIV>trajectory. The trajectory file ( .trj extension ) contains all</DIV><DIV>coordinates, velocities and forces of all the atoms in our system. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The next program we are going run is ngmx. ngmx is a very simple</DIV><DIV>trajectory viewer. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Once the ngmx program has been started you need to click on a few</DIV><DIV>buttons to view your trajectory.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>1. Once the program has been started a dialog box shows up. Click on</DIV><DIV>the box on the left of the word Protein. ( This means that we want to</DIV><DIV>view the peptide ). Then Click on the OK Button</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>2. Now we see the edges of the box with a lines drawing of the peptide</DIV><DIV>we just simulated. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>3. Select Animation in the Display menu. If you did this correctly. A</DIV><DIV>dialog box at the bottom of the screen appears. This dialog box is</DIV><DIV>used to move through your trajectory. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>4. Click on the FastForward button (two triangles pointing to the</DIV><DIV>right) and watch the peptide moving.</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>_EOF_</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>if ( $?DISPLAY ) then</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>echo Starting Trajectory viewer...</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>/nmr_apps_DarwinPPC/gromacs/bin/ngmx -f ${MOL}_md -s ${MOL}_md &</DIV><DIV>endif</DIV><DIV>#last line </DIV><DIV>**************************************************************************************************************</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Best regards</DIV><DIV>Nav</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Aug 16, 2006, at 9:42 AM, Mark Abraham wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Navratna Vajpai wrote:</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear All .. I have only recently started the GROMACS package. I want to run a MD simulation in vacuum for 5 ns say. I have tried to edit the demo file which comes with the GROMACS package. but Some how it give an error. Which I am still unable to solve. I am atttaching the file under this. Could any one please help me to move further. I am able to generate the .gro file and am able to run the pdb2gmx.<SPAN class="Apple-converted-space"> </SPAN></DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">OK at the moment you've done the analogue of calling the over-worked free car mechanic and said "My car is broken, tell me what's wrong". They are going to be much more likely to give you useful help if you tell them what you were trying to do, how you were trying to do it, and what the error was when you tried. Otherwise, they'll go and do something more interesting and/or profitable. :-)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Mark</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Kai; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Kai; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">*******************************************</SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Navratna Vajpai</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Ph. D student in Prof. Grzesiek's laboratory</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Department of Structural Biology</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Biozentrum, University of Basel</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Klingelbergstrasse 70,</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">CH-4056</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Basel, Switzerland.</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Phone- +41 61 267 2080(O)</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-tab-span" style="white-space:pre; font-family: Helvetica; "><SPAN class="Apple-style-span" style="white-space: pre; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="white-space: pre; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; white-space: pre; "><SPAN class="Apple-style-span" style="font-family: Helvetica; white-space: pre; "> </SPAN></SPAN></SPAN></SPAN></SPAN><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "> +41 78 744 0810(M)</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><A href="mailto:navratna.vajpai@unibas.ch">navratna.vajpai@unibas.ch</A></SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></DIV></BODY></HTML>