dear all,<br> can anybody tell me what happens to the velocity of intial config when i use the stochastic integrator like bd or sd.<br><br>reagrds,<br>sree.<br><br><div class="gmail_quote">On Tue, Nov 30, 2010 at 11:11 AM, Lutz Maibaum <span dir="ltr"><<a href="mailto:lutz.maibaum@gmail.com" target="_blank">lutz.maibaum@gmail.com</a>></span> wrote:<br>
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<div>On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote:<br>
> 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.<br>
<br>
</div>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.<br>
<br>
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.<br>
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-- Lutz<br>
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