Re: merge trajectory from NAMD

Date: Wed Nov 30 2005 - 21:05:19 CST

Hi Michael,

What I do is to call OPEN READ on each trajectory in turn, call TRAJ READ,
and then TRAJ WRITE into an output trajectory. It's slower than MERGE but
you can still reorient and recenter (by doing your manipulations on the
main coordinate set before writing it out) and you can define the
trajectory parameters when you do TRAJ io call. The charmm docs
have as example you can start with (see example number 3 - Copying from
one trajectory to another).


Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

On Wed, 30 Nov 2005, michael jerry wrote:

> hi, I tried to merge the multiple trajectories from NAMD using CHARMM force
> field. Because NAMD did not use the restart file, the step number in each
> NAMD trajectory file starts from 0 to 2000000 (2ns), instead of consective
> number in CHARMM, the first trajectory is 0-2000000, the second is
> 2000001-4000000, the third is 4000001-6000000.
> So, now I tried to analyze my results. I don't want to analyze each
> trajectory. But, I could not combine these three trajectory using MERGE
> command. The CHARMM always give me the first trajectory.

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