AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 29 2014 - 02:21:20 CDT

If you do not have a veldcd or dcdfreq 1-4fs, this is not possible, as you
can't reliably reconstruct velocities from coordinate frames. But you can
just extract coordinates and box size and re-equilibrate the system.

 

In VMD get frame 40000 as pdb:

 

set a [atomselect top all]

$a frame 40000

$a writepdb restart.pdb

 

Box size can be accessed with the pbc tools:

 

animate goto 40000

pbc get

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von zeynab mohamad hoseyni
Gesendet: Dienstag, 29. April 2014 06:13
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: How to extract the .coor, .vel and .xsc files for a
conformation in the middle of trajectory

 

Dear All,

 

I produced a trajectory using some advanced techniques and then I need to
run normal NPT starting from

one of the conformations of the first trajectory who shows minimum potential
energy. The point is that

i don't know how to extract the .restart.coor, .restart.vel and .restart.xsc
files of the mentioned frame

so that I start the NPT simulation. Can anyone guide on this?

 

 

All the Best,

Zeynab

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