I think that will just print a bunch of zero fields where the velocities
ought to be.
Brian
On Fri, Oct 14, 2011 at 9:09 AM, 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
> | |
> | | _______________________________________________
> | | AMBER mailing list
> | | AMBER.ambermd.org
> | | http://lists.ambermd.org/mailman/listinfo/amber
> | |
> |
> |
> |
> | _______________________________________________
> | AMBER mailing list
> | AMBER.ambermd.org
> | http://lists.ambermd.org/mailman/listinfo/amber
> |
>
> --
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 14 2011 - 06:30:04 PDT
