Hello Sir ,
Thanks for your quick reply. I have used bd_fric =0 and then my
simulation is blowing up. I have used a time step of 0.002ps, Hence i
thought if i can use some other value rather than zero but I do not know
which value to use. Can you suggest any general value for protein water
simulations.
Thanks,
Mohan
On Wed, May 29, 2013 at 4:46 PM, Dr. Vitaly Chaban <[email protected]>wrote:
> According to my understanding, setting friction coefficient is quite a
> personal thing. The higher is bd-fric, the smaller are velocities.
>
> Why not to set bd-fric = 0 in order to start with? See manual for details
> of how this trick works.
>
> Dr. Vitaly Chaban
>
>
>
>
>
> On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena <
> [email protected]
> > wrote:
>
> > Hi all,
> > I want to perform brownian dynamics simulations using gromacs
> > 4.5.5 for a system containing protein in water. What is the basis to
> > select the bd_fric value for this system. I came to know through
> previous
> > posts that a value of 3000 would be fine for a time step less than 4fs.
> My
> > question is on what basis we choose the value for bd_fric ? How does high
> > bd_fric value impact a simulation when compared to slow bd_fric value ?
> >
> >
> > Thanks for a reply in advance,
> > Mohan
> > --
> > gmx-users mailing list [email protected]
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * 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/Support/Mailing_Lists
> >
> --
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * 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/Support/Mailing_Lists
>
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* 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/Support/Mailing_Lists
