[gmx-users] How to choose bd_fric value in brownian dynamics
Mohan maruthi sena
maruthi.sena at gmail.com
Wed May 29 16:10:53 CEST 2013
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
On Wed, May 29, 2013 at 4:46 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>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 <
> maruthi.sena at gmail.com
> > 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
> > posts that a value of 3000 would be fine for a time step less than 4fs.
> > 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
> > --
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