[gmx-users] electrostatic component of the forces

[Julian Mondon-Garrec]

Thank you very much for your clear reply.

Best regards,

Julian Garrec

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.
>
> Mark


-- 
Julian Garrec, post-doc

Tel: ++41 (0)21 69 303 27
Web: https://sites.google.com/site/juliangarrec/

Laboratory of Computational Chemistry and Biochemistry
BCH 4201 Ecole Polytechnique Fédérale de Lausanne
CH-1015 Lausanne