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 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?
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>
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