[gmx-users] problem with force fields while running membrane protein simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 4 12:50:17 CET 2011

Mark Abraham wrote:
> On 4/02/2011 9:00 PM, Mohana lakshmi wrote:
>> Dear Mark
>>        I forgot to tell that i could run the same in gromacs older 
>> version i.e 3.3.3 but could not run in updated one.  I don t know the 
>> reason.  Please help me.

The tutorial is not compatible with version 3.3.3, based on the commands.  The 
expectations regarding Gromacs version are explained in the tutorial's first page.

> Please leave the context for the discussion in subsequent emails. You 
> can better remember the context of your problem than us because it is 
> more important to you than it is to us :-)
> Perhaps the tutorial is not updated for more recent GROMACS versions. 
> Perhaps you aren't using the right environment to access your multiple 
> versions of GROMACS (e.g. re-sourcing GMXRC from the other location(s)).

As far as the tutorial, it is up-to-date with instructions for 4.0.x 
(principally) and 4.5.x (via some side notes).  The problem the OP is having is 
from not following directions closely enough.  CA is a Gromos87 atomtype, being 
called from the lipid.itp nonbonded section.  Proper removal of incompatible 
parameters and subsequent extension of Gromos96 is one of the central features 
of the tutorial.


> Mark


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


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