[gmx-users] Implement a modified pull module to mdrun

Li, Hualin Hualin.Li at uth.tmc.edu
Mon Aug 12 19:29:04 CEST 2013

Hi Justin,

    Thank you for your reply. I also suspect that they may use like " change pull source code -->recomplie GROMACS -->run modified mdrun ". Do you know where the source code of the pull code is located please? 

--H L
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin Lemkul [jalemkul at vt.edu]
Sent: Monday, August 12, 2013 12:02 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Implement a modified pull module to mdrun

> Hi all,
>      I found one paper talking about they "implement a wall potential in the pull module of the mdrun program". Does anybody know how they do it please? Is it the similar method introduced in "User-specified potential functions" by using following in mdp:
> rilst = 1.0
> coulombtype   =user
> rcoulomb        = 1.0
> vdwtype        = user
> rvdw              = 1.0

I wouldn't think so.  The tabulated nonbonded potentials and the pull code are
separate entities.  If they say they modified the pull function, then that's
what the did.  I would suggest contacting the corresponding author directly.
This is the kind of question that needs to be asked directly to the people who
did the work.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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