[gmx-users] How to choose bd_fric value in brownian dynamics

[Dr. Vitaly Chaban]

Hello Mohan -

I do not use Brownian dynamics code routinely to have exact values for
various cases, but if I were you, I would start with smaller value and then
increase, until your simulation runs fine. The time-step depends not on the
method, but on characteristic oscillations (bond lengths, etc) in your
system, so maybe 2fs is just too much for your case. Although one, in
principle, can scale the force and apply a large time-step, it will not
bring any performance gain at the very end.

It is my impression that there are very few people in the community,  who
use BD engine in GROMACS. Why don't you want to use molecular dynamics?

Dr. Vitaly Chaban




On Wed, May 29, 2013 at 4:10 PM, Mohan maruthi sena
<maruthi.sena at gmail.com>wrote:

> 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 <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
>> 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
>> > --
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