Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first?
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? 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 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
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