[gmx-users] electrostatic component of the forces
julian.garrec at epfl.ch
Tue May 29 07:57:58 CEST 2012
Thank you very much for your clear reply.
Le 25/05/12 17:17, Mark Abraham a écrit :
> On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote:
>> Hi all,
>> I am trying to get the electrostatic forces acting on each atom as a
>> function of time. I have checked the list and all the suggestions are
>> based on rerunning the simulation. Is there not an easy way to print
>> these forces on the fly ?
> You can print the whole force "on the fly" with nstfout, but you
> cannot decompose it.
>> If not, what is the cleanest way to remove bonded and vdw components
>> from the forces ? One option could be to set all the unwanted
>> interaction to zero in the topology file but I am wondering if there
>> is a safer alternative.
> The code permits such a "safe" alternative, by not setting
> GMX_FORCE_BONDED, but there is no way to access that setting from the
> command line. The best you can easily do is mdrun -rerun with
> parameters zeroed.
Julian Garrec, post-doc
Tel: ++41 (0)21 69 303 27
Laboratory of Computational Chemistry and Biochemistry
BCH 4201 Ecole Polytechnique Fédérale de Lausanne
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