Mikhail Stukan wrote:
Dear gmx-users,
I am trying to simulate a thermalized wall in the framework of CG
Martini force field. To do this I am planning to link my wall atoms to
some reference points (initial positions) by harmonic potentials. From
what I have found in the manual it looks like this can be done by using
[position_restraints] declaration. What is not clear to me from the
manual is if I understand correctly that as the “reference position”
GROMACS will use the initial positions of the particles mentioned in
[position_restraints] decraration? If yes then which positions of the
Correct.
wall particles will be written out at the end of the run? The initial
ones (“reference positions”) or the instantaneous position of these
particle at the end of the run?
The instantaneous positions. Since the atoms can move using position restraints
(with the amount controlled by the force constant specified), there is no
guarantee that the positions will not change, and in fact, they usually do, even
if the amount is very small.
-Justin
Many thanks in advance,
Mikhail
=============================================
Dr Mikhail Stukan
Schlumberger Dhahran Carbonate Research Center,
Dhahran Techno Valley - KFUPM,
P.O. Box 39011, Dammam / Doha Camp 31942,
Kingdom of Saudi Arabia
Tel: +966 3 331 6182
Fax:+966 3 330 0845
mstu...@slb.com <mailto:mstu...@slb.com>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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