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--- 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 | -- --===============2861138773634211114== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber --===============2861138773634211114==--Received on Fri Oct 14 2011 - 17:30:02 PDT