[gmx-users] CG Force and Potential through do_force()

Sikandar Mashayak symashayak at gmail.com
Thu Mar 25 05:10:22 CET 2010

well if I need to add it by myself, I am not very sure in what variable to
add it to. Like I said, I know to add the force on the atom i do
f[indxofatom][XX]= forcevalue, where to potential value due to this force?


On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:
>> Hi
>> I want to do Coarse-Grained simulation in Gromacs. I have one CG force
>> formula, which I plan to implement by adding a short code in do_force()
>> routine in Gromacs 4.0.7 source code.
>> After browsing through the do_force() code, I am now familiar with data
>> structure relevant to add the new force. I mean, I can specify new force
>> by adding to f[indx][XX] and so on.
>> But I am not very sure about potential, whether do I have to explicitly
>> specify the potential on atoms due to this force or gromacs
>> automatically takes care of it by knowing the forces on each atoms?
> You will need to add that yourself if you want the reported potential to be
> accurate. GROMACS uses the given parameters in its inner loops to calculate
> energies and forces. The former are not reverse-engineered from the latter.
> If the potential is never used, however, then you can forget about it...
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100324/62930628/attachment.html>

More information about the gromacs.org_gmx-users mailing list