[gmx-users] Converting TIPS3P model to SWM4-NDP model

Justin Lemkul jalemkul at vt.edu
Wed Sep 17 13:35:31 CEST 2014

On 9/16/14 9:15 PM, Kester Wong wrote:
> Dear Justin,
> Thank you for the feedback. Yep, the converted structure is not any better than
> a starting configuration, i.e. discontinued ensemble velocitites and another
> energy minimisation for the converted structure is necessary.
> What I thought would be helpful is that for water droplet formation, users might
> save a couple of nanoseconds by having a droplet starting file, instead of a
> water box.

Anyone is welcome to contribute whatever they feel is useful in the User 
Contributions section of the website.

Conversions between polarizable and nonpolarizable models will be trivial when 
my Drude branch is ready to be merged into the main code repository, so the need 
for any hacks is very low.  Soon it will be possible to very easily do full 
biomolecular simulations with polarizable force fields just as one would with 
additive models (i.e., pdb2gmx will build everything for you).  There are a few 
lingering issues that I'm sorting out, but it should be done fairly soon.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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


More information about the gromacs.org_gmx-users mailing list