On 10/18/14 9:55 AM, James Lord wrote:
You are right it is the name of molecule type in .top, and thus no error
upon executing grompp, so index group is constructed correctly right???
In theory, but if you're saying that at t=0, LJ-SR is not zero, something is
weird. Without access to your files, it's impossible to diagnose that any further.
-Justin
rvdw=1 nm so should be fine. and for the last part I agree.
Cheers
James
On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/18/14 9:30 AM, James Lord wrote:
Hi Justin,
1. Make sure your index groups are correctly constructed.
Do I need to use make ndx? I thought just adding energygrps=protein
surface
at the end of .mdp is enough?
"Surface" isn't likely a default group (unless that's the name of the
[moleculetype]) and grompp should have raised a fatal error if the group
wasn't defined.
2. What does 5 nm correspond to? A COM distance? A minimum distance? If
the latter, then the LJ-SR energy should likely be zero, but if it's a COM
distance, that's not necessarily the case.
5 nm is minimum distance
OK, in this case, the initial LJ-SR should be zero, provided that rvdw < 5.
3. Is your PE model united-atom or all-atom? If the latter, you still
have
partial charges that will contribute to a negative Coul-SR (of course,
this
is something you can check very simply
It is all atom
Then you must have partial charges on the individual atoms and therefore
Coul-SR will be non-zero.
-Justin
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Justin A. Lemkul, Ph.D.
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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 629
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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