<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system.</div><div><br></div><div>In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. </div><div><br></div><div>CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. </div><div><br></div><div>Thank You,</div><div>Majid</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight:
bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, April 21, 2011 4:02:57 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] dna and cnt get distorted in md simulation<br></font><br>
<br><br>majid hasan wrote:<br>> Dear All,<br>> <br>> I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. <br>> My commands are:<br>> For energy minimization,<br>> <br>> grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20<br>> mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd<br>> <br>> and then I ran molecular dyamics,<br>> <br>> grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20<br>> mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd<br>> <br>> For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to
distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. <br>> I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added "nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1,<br>> Both .mdp files are placed at following addresses:<br><span>> <a target="_blank" href="http://phas.ubc.ca/~majid/md.mdp">http://phas.ubc.ca/~majid/md.mdp</a> (first .mdp file)</span><br><br>Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one.<br><br><span>>
<a target="_blank" href="http://phas.ubc.ca/~majid/lbfgs.mdp">http://phas.ubc.ca/~majid/lbfgs.mdp</a> (modified .mdp file)</span><br>> <br>> It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. <br><br>Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability.<br><br>Turn off the free energy options and see if you get stable trajectories.<br><br>-Justin<br><br>> Thanks,<br>> Majid<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a
target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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