[gmx-users] Re: gmx-users Digest, Vol 113, Issue 101

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 14:06:17 CEST 2013

On 9/23/13 3:28 AM, Jonathan Saboury wrote:
>> That said, there is an spc.itp within the AMBER subdirectories that needs
> to be
>> #included more explicitly, i.e. #include "amber99sb.ff/spc.itp"
>> May I ask why you are using SPC?  The AMBER force fields were parametrized
> with
>> TIP3P, so I see no viable reason to use a different water model.
> Ah, fixed and works like a charm, thank you :)
> To be completely honest I was using it out of ignorance. I've just been
> checking what has worked for me in tutorials and been working from there to
> something I am more interested in.

Tutorials are designed to be self-consistent (well, at least mine are) so you 
can't pick and choose.  If you change something, you risk invalidating 
everything, depending on what it is that you change.

>> It's not a bug, because genbox does not advertise such a feature.  genbox
> is
>> hard-coded to only ever deal with water.  Anything else is up to the user.
> Interesting, any reason a user would not want such a feature?

There are plenty of reasons to want it, but no one's taken the time to actually 
do it because the demand hasn't been high.  If you want something in the code, 
file a feature request on redmine.gromacs.org, or even better, propose the patch 
yourself :)

>> Any force field can be parametrized to give correct target data,
> especially for
>> a molecule as simple as cyclohexane.  What I use is a complex question,
> because
>> it depends entirely upon the task at hand :)
> Can you list a few so I can go check them out on my own? It would be
> appreciated :)

This is really a topic that can span textbook chapters.  Any attempt at a list 
would be woefully inadequate.  The best advice I can give is to read about 
different force fields and how they are applied to different molecules of 
interest.  Email cannot do the topic justice; studying the literature can.



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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