You can get a typical mdp file from some tutorials.<br>By the way, I think the topology is wrong.<br>Thanks.<br><br><br><div><span class="gmail_quote">On 7/18/07, <b class="gmail_sendername">Christopher Stiles</b> <<a href="mailto:CS145331@albany.edu">
CS145331@albany.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">I am trying to simulate a single wall CNT in a box filled
with water for about 500 ps and 300K just to start and I am having trouble with
the mdp file, basicly what should and should not be in it. I just want it
generic to start and tune it up later. Here is what I have done so far along
with links to copys of the files I have used:</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">*****************************************************************************************</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;">Must have the following files in the working directory to start:</span></font></p>
<p><font color="red" face="Times New Roman" size="3"><span style="font-size: 12pt; color: red;">SWNT_6_6_144.pdb</span></font></p>
<p><font color="red" face="Times New Roman" size="3"><span style="font-size: 12pt; color: red;">Can find a copy at: <a href="http://cs86.com/CNSE/SWNT_6_6_144.pdb" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://cs86.com/CNSE/SWNT_6_6_144.pdb</a></span></font></p>
<p><font color="red" face="Times New Roman" size="3"><span style="font-size: 12pt; color: red;"> </span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;">ffgmx.n2t </span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;">**** must change this files name to <font color="red"><span style="color: red;">ffG43b1.n2t</span></font> and add the following 2 lines:</span></font>
</p>
<p><font color="green" face="Times New Roman" size="3"><span style="font-size: 12pt; color: green;">C
C 1
C
; CNT Carbon with one bond</span></font></p>
<p><font color="green" face="Times New Roman" size="3"><span style="font-size: 12pt; color: green;">C
C 2 C
C
; CNT double bonded Carbon</span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font></p>
<p><font color="red" face="Times New Roman" size="3"><span style="font-size: 12pt; color: red;">ffgmxbon.itp</span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;">add the following line to it:</span></font></p>
<p><font color="green" face="Times New Roman" size="3"><span style="font-size: 12pt; color: green;">C C
1 0.14210 478900.</span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;">*** you can find copies of both of these files at the following
location:</span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;">/usr/local/gromacs/share/gromacs/top/</span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font></p>
<p><font color="navy" face="Times New Roman" size="3"><span style="font-size: 12pt; color: navy;">x2top -f SWNT_6_6_144.pdb -o
SWNT_6_6_144.top -r SWNT_6_6_144.rtp</span></font></p>
<p><i><font color="red" face="Times New Roman" size="3"><span style="font-size: 12pt; color: red; font-style: italic;">***Note: for some reason
it does not generate SWNT_6_6_144.rtp</span></font></i></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font></p>
<p><font color="navy" face="Times New Roman" size="3"><span style="font-size: 12pt; color: navy;">editconf -f SWNT_6_6_144.gro -o
SWNT_6_6_144.gro -d 0.5</span></font></p>
<p><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font></p>
<p><font color="navy" face="Times New Roman" size="3"><span style="font-size: 12pt; color: navy;">genbox -cp SWNT_6_6_144.gro -cs -o
SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxsol 300</span></font></p>
<p><i><font face="Times New Roman" size="3"><span style="font-size: 12pt; font-style: italic;"> </span></font></i></p>
<p><font color="navy" face="Times New Roman" size="3"><span style="font-size: 12pt; color: navy;">grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro
-p SWNT_6_6_144.top -o -maxwarn 310</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">***********************************************************************************************</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">#### em3.mdp### </span></font><font color="red"><span style="color: red;">Can find a copy at: <a href="http://cs86.com/CNSE/em3.mdp" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://cs86.com/CNSE/em3.mdp</a></span></font><font color="red"><span style="color: red;"></span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">title
= SWNT_6_6_144</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">cpp
= cpp</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">include
= /usr/local/gromacs/share/gromacs/top/</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">define
= -DFLEX_SPC</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">integrator
= md</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">dt
= 0.002</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nsteps
= 500000</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nstxout
= 5000</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nstvout
= 5000</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nstlog
= 5000</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nstenergy
= 250</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nstxtcout
= 250</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">xtc_grps
= Protein</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">energygrps
= Protein SOL</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">nstlist
= 10</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">ns_type
= grid</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">rlist
= 0.8</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">coulombtype
= cut-off</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">rcoulomb
= 1.4</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">rvdw
= 0.8</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">tcoupl
= Berendsen</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">tc-grps
= Protein SOL</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">tau_t
= 0.1 0.1</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">ref_t
= 300 300</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Pcoupl
= Berendsen</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">tau_p
= 1.0</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">compressibility
= 4.5e-5</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">ref_p
= 1.0</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">gen_vel
= yes</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">gen_temp
= 300</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">gen_seed
= 173529</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">constraints
= all-bonds</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">**************************************************************************</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">This is what I get after running grommp:</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">-bash-3.00$ grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144.top -o -maxwarn 310</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">
:-) G R O M A C S (-:</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">.</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">.</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">.</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> -[no]renum bool
yes Renumber atomtypes and minimize number of</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">
atomtypes</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">creating statusfile for 1 node...</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable integrator, using 'md'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
'l-bfgs' 'tpi'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable ns-type, using 'Grid'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'Grid' 'Simple'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable coulombtype, using 'Cut-off'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'Cut-off' 'Reaction-Field'
'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift'
'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable tcoupl, using 'No'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes'
'Andersen' 'Andersen-interval'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable Pcoupl, using 'No'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman'
'Isotropic'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable gen-vel, using 'no'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'no' 'yes'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' for variable constraints, using 'none'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Next time use one of: 'none' 'h-bonds' 'all-bonds'
'h-angles' 'all-angles'</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Back Off! I just backed up mdout.mdp to ./#mdout.mdp.15#</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">checking input for internal consistency...</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">...ling cpp</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">: command not found</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">cpp exit code: 32512</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> SWNT_6_6_144.top > gromppOpff2m'cs/top -DFLEX_SPC</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">' command is defined in the .mdp file</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">processing topology...</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">processing coordinates...</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">-------------------------------------------------------</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Program grompp, VERSION 3.3.1</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Source code file: futil.c, line: 340</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">File input/output error:</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">conf.gro</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">-------------------------------------------------------</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">"This May Come As a Shock" (F. Black)</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">***********************************************************************************</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;">Any help or advice is greatly appreciated!</span></font></p>
<p><font face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial;"> </span></font></p>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;">~Christopher Stiles </span></font></pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">College</span></font> of Nanoscale Science and Engineering (CNSE)
</pre><pre><font face="Courier New" size="2"><span style="font-size: 10pt;">State University of New York, Albany, New York 12203, USA</span></font></pre></div>
</div>
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>James Jianzhang<br>Department of Mechanical and Chemical Engineering <br>North Carolina Agricultural and Technical State University <br>1601 East Market Street
<br>Greensboro, NC 27411 <br><a href="mailto:jzhang@ncat.edu">jzhang@ncat.edu</a> or <a href="mailto:james.zhangj@gmail.com">james.zhangj@gmail.com</a><br><a href="http://www.ncat.edu/~jzhang">http://www.ncat.edu/~jzhang</a>