[gmx-users] Position restraints

Mikhail Stukan mstukan at slb.com
Sat Apr 9 17:23:07 CEST 2011

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,

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
mstukan at slb.com<mailto:mstukan at slb.com>

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