Re: Time step is incompatible in the NAMD DCD file analyzed with CHARMM

From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Wed Jun 18 2008 - 16:35:42 CDT

Technically, you should direct you question to the CHARMM forum;
however, I suspect they will tell you to direct it to the NAMD forum.
Short answer is you should probably be OK; try writing out frames from
CHARMM
with (e.g.)

nobomb
traj read
write coor card name test.cor

and looking at it in VMD

Victor

On Wed, 2008-06-18 at 14:42 -0500, tw shen wrote:
> Hi,
>
> I did a simulation trajectory for 1 ns with the integration
> time step of 2 fs with NAMD 2.6. However, when I tried
> to read the trajectory with CHARMM, it shows that
>
> CHARMM> open unit 51 read unform name "prod01.dcd"
> VOPEN> Attempting to open::prod01.dcd::
> OPNLGU> Unit 51 opened for READONLY access to prod01.dcd
>
> CHARMM> traj query unit 51
>
> READING TRAJECTORY FROM UNIT 51
> NUMBER OF COORDINATE SETS IN FILE: 1000
> NUMBER OF PREVIOUS DYNAMICS STEPS: 500
> FREQUENCY FOR SAVING COORDINATES: 500
> NUMBER OF STEPS FOR CREATION RUN: 500000
>
> NUMBER OF DEGREES OF FREEDOM: 0
> NUMBER OF FIXED ATOMS: 0
> THE INTEGRATION TIME STEP (PS): 0.0409
> THE FILE CONTAINS CRYSTAL UNIT CELL DATA
> THE FILE DOES NOT CONTAIN 4-D DATA
>
> The time step is 0.0409 ps recorded in the dcd file, and the
> degrees of freedom are not supposed to be zero. Will that
> cause a problem when I analyze the trajectory? Thank you
> in advance.
>
> Tsaiwei Shen
>

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