[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

majid hasan pu_majidhasan at yahoo.com
Wed Apr 20 20:58:57 CEST 2011

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,

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at 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:



> Thank You,
> Majid

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

-- gmx-users mailing list    gmx-users at gromacs.org
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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110420/02696a09/attachment.html>

More information about the gromacs.org_gmx-users mailing list