<div>Hi ! </div>
<div>I am attempting to do a simulated annealing and running into problem. </div>
<div>Let me give a introduction to my system. I have a segment of a protein that was not crystallographyically resolved, but was later resolved by NMR. </div>
<div>So I ligated the NMR structure to the crystal structure and in an attempt to <font style="BACKGROUND-COLOR: #ffffff">find the correct orientation</font> of the NMR <font style="BACKGROUND-COLOR: #ffffff">segment in the crystal structure I planned to do a simulated annealing run specifically to this ligated NMR segment. Having ligated this NMR segment to the crystal structure I gave the pdb2gmx command, then created a box, filled it with water and performed a distance restrained energy minimization (wherein I input some FRET distances as distance restraints). Its all fine till this step. Now I create an index group that has the NMR group as the third group in the temperature coupling, the other two are Protein and Non-Protein. when I run the grompp to start a simulated annealing run I get a message stating that the NMR group's atoms are also found in the Protein group. Gromacs is right in detecting this problem. As I cannot have the same amino acids in 2 different groups which are coupled to two different temperatures. So how am I to attempt this simulated annealing because the program does not want to have the NMR group present in the Protein group</font>?</div>
<div>So say I delete the NMR segment that was appended to the crystal structure how and which stage do I integrate the NMR group that I wanted to perform the simulated annealing on, into the system?</div>
<div> Thanks</div>
<div>Jayant</div>
<div> </div>
<div><font color="#ff0000"><strong>The pr.mdp file is as below</strong></font></div>
<div><font color="#ff0000"></font> </div>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; Berendsen temperature coupling is on in two groups</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Tcoupl<span style="mso-spacerun: yes"> </span>= Berendsen </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">tc-grps<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>Protein<span style="mso-tab-count: 1"> </span>Non-Protein<span style="mso-spacerun: yes"> NMR-group </span><span style="mso-spacerun: yes"> </span></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">tau_t<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0.1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>0.1<span style="mso-spacerun: yes"> </span>0.1</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">ref_t<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>300<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>300<span style="mso-spacerun: yes"> </span>300</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; Energy monitoring</span></p>
<div class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">energygrps<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>Protein<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>Non-Protein<span style="mso-spacerun: yes"> </span>NMR-group</span></div>
<div class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></span><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; Pressure coupling is not on</span></div>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Pcoupl<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>parrinello-rahman</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">tau_p<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0.5</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">compressibility<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>4.5e-5</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">ref_p<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>1.0</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; Generate velocites is on at 300 K.</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">gen_vel<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>yes</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">gen_temp<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>300.0</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">gen_seed<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>173529</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;simulated annealing</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;Type of annealing form each temperature group (no/single/periodic)</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">annealing<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>=<span style="mso-tab-count: 1"> </span>no<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>single</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;Number of annealing points to use for specifying annealing in each group</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">annealing_npoints<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>9</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">;</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; List of times at the annealing points for each group</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">annealing_time<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0 25 50 75 100 125 150 175 200</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">; Temp.at each annealing point, for each group.</span></p>
<div class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">annealing_temp<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>300 350 400 450 500 450 400 350 300</span></div>
<div class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></span> </div>
<div class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><font color="#ff0000"><strong>The error messge is given below</strong></font></span></div>
<div class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></span>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">creating statusfile for 1 node...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">checking input for internal consistency...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">calling /usr/bin/cpp...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">processing topology...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Generated 279 of the 1225 non-bonded parameter combinations</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Excluding 3 bonded neighbours for Protein_D 1</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Excluding 2 bonded neighbours for SOL 72948</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Excluding 1 bonded neighbours for NA+ 214</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Excluding 1 bonded neighbours for CL- 207</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">processing coordinates...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">double-checking input for internal consistency...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Velocities were taken from a Maxwell distribution at 300 K</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">renumbering atomtypes...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">converting bonded parameters...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>G96BONDS:<span style="mso-spacerun: yes"> </span>4588</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>G96ANGLES:<span style="mso-spacerun: yes"> </span>6638</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>PDIHS:<span style="mso-spacerun: yes"> </span>2521</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>IDIHS:<span style="mso-spacerun: yes"> </span>2044</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>LJ14:<span style="mso-spacerun: yes"> </span>7634</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>DISRES:<span style="mso-spacerun: yes"> </span>22</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#<span style="mso-spacerun: yes"> </span>SETTLE:<span style="mso-spacerun: yes"> </span>72948</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">initialising group options...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">processing index file...</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">WARNING 1 [file "new.top", line 28039]:</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>T-Coupling group Protein has fewer than 10% of the atoms (4550 out of</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>223817)</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>Maybe you want to try Protein and Non-Protein instead?</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">WARNING 2 [file "new.top", line 28039]:</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>T-Coupling group Non-Protein has fewer than 10% of the atoms (2 out of</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>223817)</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>Maybe you want to try Protein and Non-Protein instead?</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">-------------------------------------------------------</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Program grompp, VERSION 3.3.3</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Source code file: readir.c, line: 843</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Fatal error:</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">Atom 2589 in multiple T-Coupling groups (1 and 3)</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">-------------------------------------------------------</span></p></div>
<div><font color="#ff0000"><strong></strong></font> </div>
<div><font color="#ff0000"><strong></strong></font> </div>
<div><font color="#ff0000"><strong>The commands that I use are given below</strong></font></div>
<div><strong><font color="#ff0000"></font></strong> </div>
<div><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#pdb2gmx -f start.pdb -p new<span style="mso-spacerun: yes"> </span>-o new -ignh -merge</span></div>
<div>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#creating a box and addition of water molecules</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#editconf -f new.gro -o out -c<span style="mso-spacerun: yes"> </span>-princ -d 2.2</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#genbox -cp out -cs -o check</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#editconf -f check<span style="mso-spacerun: yes"> </span>-o check.pdb</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#rasmol check.pdb</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#Energy minimization and addition of ions to neutralise the system</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#grompp -f em.mdp -c check -p new.top -o em.tpr</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#genion -s em.tpr -o next<span style="mso-spacerun: yes"> </span>-p new -random -g -neutral -conc 0.15 #pname -Na -np 13</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#editconf -f next.gro -o next.pdb</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#rasmol next.pdb</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#option 13 for SOL</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#Running the EM. Here change the Na to NA+ in topology<span style="mso-spacerun: yes"> </span>file and I/P *.gro file.</span></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#grompp -f em.mdp -c next.gro -p new.top -o em.tpr</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#mdrun -v -s em -x em -o em -c em.gro &</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#editconf -f em.gro -o em.pdb</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#rasmol em.pdb</span></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><strong><font color="#ff0000">This is where the problem begins</font></strong></span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#Running MD. </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">grompp -f pr.mdp -c em.gro -o pr.tpr -p new.top -n index</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#mdrun -s pr -e pr -g md -o traj.trr -c pr.gro &</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"> </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#extending</span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#tpbconv -s ../pr.tpr -f 300.xtc<span style="mso-spacerun: yes"> </span>-e ../ener.edr -o 1ns.tpr -until 1000 </span></p>
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">#mdrun -s 1ns.tpr -o 1ns.trr &</span></p><br clear="all"><br>-- <br>Jayasundar Jayant James<br>
<br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br></div>