I think you do not use the bd_fric in combination with sd, but with bd,
the friction is set by the tau_t instead. Did you als use different
parameters for that?
For bd, you would use the friction bd_fric to set the ld friction, but
not for sd, but I could be wrong here...
Gerrit
syma wrote:
Hi,
I have been having a few problems running Langevin dynamics and was
wondering if anyone can help.
I have run both atomistic and coarse grain LD simulations in gromacs 3.1 3.2
and 3.3. The puzzling thing is that changing the value of the frictional
constant makes no difference to the simulations. Ie RMSD values are EXACTLY
the same when simulations are run with different frictional constants.
I have used gmxdump to analyse the tpr files- the correct values for the
frictional term does seem to be picked up. The mdp file I have been using is
attached. If anyone can see anything obviously wrong with the file I would
appreciate your advice.
Best wishes,
-Syma
***************************************************
Dr Syma Khalid
Department of Biochemistry,
University of Oxford
South Parks Road,
Oxford
OX1 3QU
U.K.
***************************************************
------------------------------------------------------------------------
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