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
--
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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