Dear Amber users,
I ran a REMD simulation of a 16mer peptide in
explicit solution using 24 replicas in the temperature range between
300-400K for 40ns. The simulation ran properly with a exchange
frequency between 20-30%. I then tried to extract the temperature
trajectory at 300K using the script provided in the amber tutorial
http://ambermd.org/tutorials/advanced/tutorial7/
Here is the scriptI used:
----------------------------------------------------------------------------
#!/bin/csh
ptraj ../../peptide.parmtop << EOF
trajin ../../production/remd.mdcrd.001 remdtraj remdtrajtemp 300.0
trajout remd.300K.mdcrd nobox
go
EOF
---------------------------------------------------------------------------
I am expecting 40000 (since the simulation is for 40ns) coordinate
sets for each of the 24 replicas. I am however not able to extract the
entire coordinate sets
For the replica at 300K, I get only 63 sets and there is an error message:
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: remd.300K.mdcrd
If this is not a compressed file then there is a problem
I am not exactly sure the cause of this problem.
For your information, I ran the simulation using 192 processors (8
processor per replica). Prior to running the REMD, I also did a 200 ps
equilibration for each of the 24 replicas at their specified
temperatures using 96 processors (4 processor per replica).
Could this change in processor number of the separate run be a
possible cause of the error?
I will be glad if anyone can kindly guide me on this.
Thank you,
Dilraj.
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Received on Mon Jul 02 2012 - 05:30:05 PDT
