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robin
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Original Post (Thread Starter)
#26445 02/04/2011 3:39 PM
by kittim
kittim
Dear Charmmers,

Suppose I forgot to write rst file.
Can I get one from the dcd?

Typical input will be as follows (shown the DYNA part only)

------------------------------

open write name traj.dcd unit 32

dyna cpt leap star time 0.002 nstep 20000 iseed 111111 nprint 5000 nsavc 5000 -
pconst pmxx 100. pmyy 100. pmzz 100. pref 1. -
hoover reft 300. tmass 1000. -
nsavv 0 inbfrq -1 iprfrq 100 -
iunrea -1 iunwri -1 iuncrd 32 iunvel -1 kunit -1 -
iasors 0 iasvel 1 iscvel 0 ichecw 0 echeck 1000

Thank you in advance -
laugh
Liked Replies
by rmv
rmv
Specifically, the restart file contains coordinates, delta coordinates, velocities, integrator state information, etc. A binary trajectory file, sometimes called a 'dcd' file by people with limited CHARMM experience (I use .trj extension), contains only coordinates.

You can get a restart file (I use .res, but the extension is irrelevant) after the dynamics run since that's when it is normally written, but the proper DYNAmics setup is required; OPEN the file, and point to the integer unit number via the 'IUNWRI integer' option.

In summary, it cannot be done from just coordinates, and the best advice is still to repeat the initial run with the correct setup.
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