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shane yue
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Original Post (Thread Starter)
Reading DCD trajectory using MPI CHARMM #38114 11/01/2020 4:34 PM
by shane yue
shane yue
Hi CHARMM users,

Hope all goes well.

I am trying to do some time-consuming analyses on our clusters using a CHARMM (c42b2) compiled with MPI.

When I read a DCD trajectory I got the fatal error:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CHARMM> ! Loop, calculate INTER
CHARMM> ! ---------------------------
CHARMM> set i = 1
Parameter: I <- "1"

CHARMM>

CHARMM> label loop

CHARMM> traj read ! read trajectory

READING TRAJECTORY FROM UNIT 11
NUMBER OF COORDINATE SETS IN FILE: 498
NUMBER OF PREVIOUS DYNAMICS STEPS: 1
FREQUENCY FOR SAVING COORDINATES: 1
NUMBER OF STEPS FOR CREATION RUN: 498

TITLE> Created by DCD plugin^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
TITLE> REMARKS Created 08 July, 2020 at 23:45^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
TITLE> * DATE: 11/ 1/20 9:56:40 CREATED BY USER: zhiyue
TITLE> *

***** LEVEL -5 WARNING FROM *****
***** READ errorno -1 for traj_0_0.dcd: 498 frames expected but 0 frames read
*******************************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The original DCD trajectory was generated by NAMD and processed with VMD PBCTools Plugin. But it was read successfully by a non-MPI CHARMM on the cluster. So I suspect the trajectory itself should be fine.

Thus, my questions are:

1) Can MPI CHARMM read DCD trajectory (with only one CPU requested)?
2) If yes, is there any special requirement (especially on CHARMM) to make it work?

Thanks in advance.

All the best
Liked Replies
Re: Reading DCD trajectory using MPI CHARMM #38119 Nov 1st a 08:45 PM
by rmv
rmv
I recently used TRAJ READ in a loop, with a c43b1 MPI executable using 16 cores so that I could do an ENERGY call, then a series of INTE commands to compute peptide:membrane interactions.
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