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
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========================================
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
========================================
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