[gmx-users] langevin dynamics

[David Mobley]

Gerrit is right, with "sd", the friction is set by tau_t, as described
in the section on SD in the manual. In my hands, different tau_t with
sd does make a significant difference in what goes on...

David


On 7/31/06, Gerrit Groenhof (RUG) <g.groenhof at rug.nl> wrote:
> 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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