d_aghaie at yahoo.com
Sun Feb 6 10:43:16 CET 2011
Dear gromacs users
I am using hpc system of our university to work on molecular dynamics simulation with gromacs. The gormacs has been installed there and I can connect to the hpc system and submit my jobs.
Now I want to know that for using gnuplot to have my graphs, the gnuplot program should be installed on my office pc or on the hpc system and let me know how to do that? If it should be installed on hpc let me know pls. how should it be installed ?
Thanks for your time
--- On Sat, 2/5/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Porting Amber parmbsc0 force field to Gromacs
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, February 5, 2011, 8:53 PM
william Stebbeds wrote:
> I would like to use the parmbs0 Amber forcefield to Gromacs, specifically the nucleic acid parameters.
> Is this likely to come in a future release?
Force fields are only implemented if a developer has a compelling reason to do so, and then take the time to validate it. As such, new force fields are not often introduced.
> I appreciate that this will likely be a difficult process but if anyone can point me in the right direction I would be very grateful.
You can probably take an existing Amber force field and modify it. Chapter 5 is your friend here. By modifying existing files, you don't have to come up with all the syntax by yourself.
> Will - Cranfield University
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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