On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote:
you think it was the cofactor model?
If you're using a CHARMM-parametrized cofactor with an Amber99SB protein, I'd
say the simulations are wholly unreliable. It's certainly the #1 likely cause
for nonsensical results. If you want to get to the root of the issue, you need
to start with a solid foundation.
Unless that's not what your last message meant? When you say "only changed the
cofactor," that implied to me that you didn't consistently convert everything in
the system.
-Justin
On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote:
wait, I only changed the cofactor to gromacs charmm27.ff format
Pretty amazing that the simulation even ran with that mash-up of
parameters :)
I'd say that's the most likely cause of your problems; nonsensical
physical model leads to nonsensical output.
-Justin
On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:
I suppose something might be wrong with the simulations. I am using
gromacs 4.6.5, I am simulating a protein with a cofactor, someone else
parametrized it, I changed from charmm to gromacs amber99sb.ff format
with
a script on the gromacs website. I did a typical em/nvt/npt
equilibration
followed by a 5 ns production run. I picked 250 frames out of the
trajectory, and altered them to the TPIC input format with a script I
wrote, to insert the particle half way between two atoms that I chose. I
am
inserting a water molecule. When I run the actual insertion some of the
frames have a reasonable looking mu, and some have -inf mu. I think it
may
have to do with cavity size, some frames have too small of a cavity, so
the
interaction energy of the inserted water diverges...
On Mon, Jun 9, 2014 at 6:40 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote:
Hi all, I am having a problem with -inf mu coming out of TPIC
calculations.
Anyone have some suggestions on how to avoid this? Tabulated
potentials?
Or
can I modify the source code to reject the absurd values that cause
this? I
read a few old discussions on this, I didnt see much on how to handle
this.
I'd be much more concerned that something is going wrong in the
simulations. I have no experience with TPIC, but if you post more
detailed
information about what you're doing and which Gromacs version you're
using,
you're more likely to get some suggestions.
-Justin
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==================================================
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.
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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