AMBER Archive (2008)

Subject: Re: AMBER: initial velocities of MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 13 2008 - 11:59:26 CDT

yes you can, but it also may depend on the initial structure.
is it from experiment, or was part of it a model? if model, then
you might want to generate a different model and compare
the results. if the structure is from expt, then you might want to check
carefully your equilibration protocol and make sure it is slow enough and
that you used enough phases of reducing restraints. equilibration can be
very tricky, but it's hard to say more without knowing the details of your
initial structure.

you change the initial velocities by changing the random number seed ig,
check the manual for details. you need to set tempi>0 for that to work.

On Tue, May 13, 2008 at 12:37 PM, Jena M <jeninhas_at_hotmail.com> wrote:
>
>
>
> Hi,
>
>
>
> I have run a MD simulation of a protein and the trajectory revealed
> instabilities in some regions of that protein. So I would like to ran the MD
> simulation again but using different initial velocities, in order to see if
> I these instabilities are kept. Does anyone know how to change the initial
> velocities? Can I use the same top and crd files to initiate the
> equilibration phase?
>
>
>
> Thanks a lot,
>
> Jena
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