<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 style="font-family: 'times new roman', 'new york', times, serif; ">Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD.</div><div style="font-family: 'times new roman', 'new york', times, serif; "><meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; "><font class="Apple-style-span" size="2"> <span><a target="_blank" href="http://phas.ubc.ca/~majid/md.mdp">http://phas.ubc.ca/~majid/md.mdp</a></span></font></span></div><div style="font-family: 'times new roman', 'new york', times, serif; "><span class="Apple-style-span"
style="font-family: arial, helvetica, sans-serif; "><font class="Apple-style-span" size="2"><br></font></span></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">and here is what I see by running .trr files obtained from EM, and MD.</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">On running EM.trr file:</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. </font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">On running MD.trr file:</font></div><div><font
class="Apple-style-span" face="arial, helvetica, sans-serif">CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation.</font></div><div style="font-family: 'times new roman', 'new york', times, serif; "><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; "><font class="Apple-style-span" size="2"><br></font></span></div><div style="font-family: 'times new roman', 'new york', times, serif; "><font class="Apple-style-span" size="2"><br></font></div><div style="font-family: 'times new roman', 'new york', times, serif; ">Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent.</div><div style="font-family: 'times new roman', 'new york', times, serif;
font-size: 12pt; "><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Thanks,</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Majid<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> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, April 21, 2011 10:25:35 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>> 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.<br>> <br><br>The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each.<br><br>> 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. <br><br>So, the "first" .mdp file is the one that actually specifies an MD run, not EM? Or does "first" correspond to the order
of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators.<br><br>> CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. <br><br>Bonds don't break or form during classical MD. Any bonds "forming" or "breaking" are simply a visualization artifact since you're not reading a topology into the visualization software.<br><br>From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion.<br><br>-Justin<br><br>> Thank You,<br>> Majid<br>> <br>>
------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Thu, April 21, 2011 4:02:57 AM<br>> *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation<br>> <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><span> <<a target="_blank"
href="http://vt.edu">http://vt.edu</a>> | (540) 231-9080</span><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> <mailto:<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" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br><span>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><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]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a
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