[gmx-users] 4-site rigid body model

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 19 01:37:36 CET 2010

Sanku M wrote:
> Hi,
>   I have a molecule consisting of 4 sites  which have fixed relative 
> positions interacting only through LJ and coulomb interaction.  I was 
> wondering how can I do MD simulation in GROMACS keeping the geometry 
> unchanged .  Is just putting constraints along  all the possible 
> distances  and using LINCS good enough for maintaining the geometry ? Or 

I suspect it is, and I would imagine it would be easy enough to determine that 
with a short test.

> , Does one need to also make sure the angles are also unchanged but I am 
> not sure how to do that ?  I was wondering what will be an optimum ways 

You can also set "constraints = all-angles" in the .mdp file.

> of dealing with such  a 4-site system. I guess, Settle can not be used 
> for such a 4-site system.

Nope, SETTLE shouldn't be relevant here.


> Thanks
> Sanku


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list