From: sunyeping (sunyeping_at_aliyun.com)
Date: Thu Nov 12 2015 - 20:57:20 CST
Hi, Felipe,
Thank you. I guess we could continue a MD without the vel file if we specify the temperature. Usually I specify the vel file and comment out the "temperature" option when I continue a MD. Would the atom velocities be calculated automatically in the program with the specified temperature?
Yeping------------------------------------------------------------------From:Felipe Merino <felipe.merino_at_mpi-dortmund.mpg.de>Time:2015 Nov 12 (Thu) 21:48To:namd-l <namd-l_at_ks.uiuc.edu>, 孙业平 <sunyeping_at_aliyun.com>Subject:Re: namd-l: Would it be possible to continue a simulation from any snapshot of a trajectory?
Hi,
The coordinates and box information are stored in the dcd file, so
creating restarts for that should not be a problem. However, the
velocities cannot be recovered from the trajectory itself. So unless
you specifically saved a velocity trajectory you won't have the vel
file and therefore will need to re-assign velocities from scratch.
Depending on what you want from the trajectory, that might not be an
appropriate restart.
Best
Felipe
On 12/11/15 09:45, sunyeping wrote:
Dear all,
A NAMD simulation can be continued
from where it break. But
would it be possible to continue a simulation from any snapshot of a trajectory?
In another word, could it be possible to prepare the .coor,
.vel, and .xsc extend files from any timestep from the
trajectory?
Best regards.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306
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