[gmx-users] changing the velocity in trajectory file

[sreelakshmi ramesh]

dear all,
              can anybody tell me what happens to the velocity of intial
config when i use the stochastic integrator like bd or sd.

reagrds,
sree.

On Tue, Nov 30, 2010 at 11:11 AM, Lutz Maibaum <lutz.maibaum at gmail.com>wrote:

> On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote:
> > Lutz ya you are true but as you said how can i change the velocity  for a
> config every move as in TPS?since i have not done tps i have no idea abt
> this.
>
> You can't, neither for TPS nor for FFS. I don't think Gromacs provides this
> functionality. You will have to write your own code that reads positions and
> velocities from a trajectory file, modifies the velocities, and writes
> positions and velocities to a file that Gromacs can use as an initial
> configuration.
>
> Alternatively, you can use a stochastic integrator (like Brownian dynamics)
> and set ld_seed to -1. This way, even identical initial configurations will
> result in different trajectories.
>
>  -- Lutz
>
>
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