[gmx-users] Replica exchange with scaled topology files

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 3 22:48:49 CET 2010

On 4/11/2010 1:53 AM, Sai Pooja wrote:
> Hi,
> I am running a the gromacs Replica exchange (NVT). However along with 
> the temperatures, I have also scaled a few paramters in the topology 
> file for each of the replicas for generating the .tpr files. 
> Everything seems to be running fine but is this a valid thing to do? 
> Or would gromacs simply ignore those differences?

mdrun does whatever the .tpr and command line options tell it. mdrun 
knows about nothing (e.g. the forcefield files) that would permit it 
recognize a "difference". Even if it could recognize such, silently 
doing something else would be the way madness lies... grompp is pretty 
good at noticing things that might be astray and giving suitable feedback.


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