[gmx-users] Re: Error : There is no domain decomposition for ....

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 30 13:48:05 CEST 2010

----- Original Message -----
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Date: Thursday, September 30, 2010 21:43
Subject: [gmx-users] Re: Error : There is no domain decomposition for ....
To: gmx-users at gromacs.org

> Mark, 
> These long range parameters have been used by Bjelkmar et 
> al.  in their recent paper [1]for simulations of CHARMM ff 
> in GROMACS. So I use it ! 
> [1] Bjelkmar, P., P. Larsson, et al. (2010). "Implementation of 
> the CHARMM Force Field in GROMACS: Analysis of Protein Stability 
> Effects from Correction Maps, Virtual Interaction Sites, and 
> Water Models." J. Chem. Theory Comput. 6(2): 459-466.

I'm not questioning any .mdp file settings. However the combination of topology and initial coordinates contains some kind of bonded interaction between atoms that are much further apart than you would normally suppose. You should explore what is going on there.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100930/62c76cfd/attachment.html>

More information about the gromacs.org_gmx-users mailing list