<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>Okay, thanks a lot.</div><div><br></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> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, April 20, 2011 12:01:33 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt<br></font><br>
<br><br>majid hasan wrote:<br>> Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first?<br>> <br><br>You should always run energy minimization. What I'm saying is that you should not expect to see any major changes or important phenomena evolve when simply running EM.<br><br>> And one more thing, any idea how long it may take to run md for 367 atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it is possible to get any results from mdrun on laptop?<br>> <br><br>You can get results, but that depends entirely upon how much of the processor is being used to do other things at the same time. For a small system, running locally may be an option, but for anything larger than a few hundred atoms you're better off running on a real cluster to avoid performance loss. It will certainly "work," but probably not as fast as you might need for very long
simulations.<br><br>-Justin<br><br>> Thanks again,<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:* Wed, April 20, 2011 11:47:09 AM<br>> *Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt<br>> <br>> <br>> <br>> majid hasan wrote:<br>> > Dear All,<br>> ><br>> > I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide
me what can be the possible issues here, and how can I improve it?<br>> ><br>> <br>> Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods.<br>> <br>> > Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations.<br>> ><br>> <br>> Always start with the primary literature:<br>> <br>> <a target="_blank" href="http://dx.doi.org/10.1002/prot.22711">dx.doi.org/10.1002/prot.22711</a><br>> <br>> -Justin<br>> <br>> > Thank You,<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> <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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