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) <[EMAIL PROTECTED]> 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.
>
>
>
>***************************************************
>
>
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>gmx-users mailing list [email protected]
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to [EMAIL PROTECTED]
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
