The crd file (mdcrd, amber trajectory, written at intervals specified by
ntwx) doesn't contain velocities, unless you specifically specify this by
setting ntwv=1.
See the manual secction 2.6.3.
Marc
On 14 October 2011 14:09, Antje Wolf <antje.wolf.scai.fraunhofer.de> wrote:
> But if I use ptraj's trajout restart command to generate a new restart file
> from the last frame of my crd file, the velocity should be written out,
> shouldn't it?
>
> ----- Ursprüngliche Mail -----
> | It holds for MD in general, not sure what SMD is or what degree of
> | equilibration is required for it. Going from velocity = 0 to 300K
> | without equilibration is like having your car pool ride drive through
> | the house and scoop you out of bed without slowing down.
> |
> | Bill
> |
> | ---
> |
> | does this hold only for SMD or for any kind of MD? I always thought a
> | restart file is simply writing out coords and velocities in regular
> | intervals. So what is the difference then from using the last
> | snapshot saved in the crd file?
> |
> | Antje
> |
> | ----- Ursprüngliche Mail -----
> | | > You can pick the last frame form the mdcrd and create your new
> | | > restart.
> | |
> | | Note that if you do this, you will have to re-equilibrate from
> | | scratch.
> | |
> | | Bill
> | |
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> |
> |
> |
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>
> --
> Antje Wolf
>
> Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> Department Bioinformatics
> Schloss Birlinghoven
> D-53754 Sankt Augustin
>
> Tel.: +49 2241 14 2552
> E-mail: antje.wolf.scai.fraunhofer.de
> Internet: http://www.scai.fraunhofer.de
>
>
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Received on Fri Oct 14 2011 - 06:30:05 PDT
