Okay, thanks a lot. Majid
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@gromacs.org> Sent: Wed, April 20, 2011 12:01:33 PM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: > Okay, thanks. But then does it make any big difference on mdrun if we don't >minimize energy first? > 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. > 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? > 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. -Justin > Thanks again, > Majid > > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <jalem...@vt.edu> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *Sent:* Wed, April 20, 2011 11:47:09 AM > *Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to wrapping >of dna around cnt > > > > majid hasan wrote: > > Dear All, > > > > 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? > > > > Energy minimization and dynamics are independent processes. You should not >expect large structural changes during EM with any of the methods. > > > Moreover, what is the right value of nstlist for amber99sb-ildn forcefield >for md simulations. > > > > Always start with the primary literature: > > dx.doi.org/10.1002/prot.22711 > > -Justin > > > Thank You, > > Majid > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or >send it to gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists