From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Nov 24 2016 - 11:07:06 CST
Hi Kaushik,
Why is this line commented out?
#paraTypeCharmm on
The default for NAMD, if this is not included, is for the parameters to be specified in XPLOR format (see http://www.ks.uiuc.edu/Research/namd/2.12b1/ug/node12.html#1810), which is not the format CHARMM parameter files use, and would be why the parser is complaining about an unknown parameter in an XPLOR parameter file.
Josh Vermaas
Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>
On Nov 23, 2016, at 12:58 PM, kaushik chakraborty <kaushik290187_at_gmail.com<mailto:kaushik290187_at_gmail.com>> wrote:
Hi,
I am trying to run a REMD simulation of a with CHARMM 22 force field . I am getting the following error massage.
Charm++> Running on MPI version: 3.0
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 4
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Charm++> TORUS A SIZE 4 USING 0 1 2 3
Charm++> TORUS B SIZE 1 USING 0
Charm++> TORUS C SIZE 1 USING 0
Charm++> TORUS MINIMAL MESH SIZE IS 4 BY 1 BY 1
Redirecting stdout to files output/0/.d0.log through 3
------- Partition 1 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 1 FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE par_all22_prot_cmap.inp
LINE=**>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<*
------- Partition 2 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 2 FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE par_all22_prot_cmap.inp
LINE=**>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<*
------- Partition 3 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 3 FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE par_all22_prot_cmap.inp
LINE=**>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<*
------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 0 FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE par_all22_prot_cmap.inp
LINE=**>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<*
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
Here I am using the replica.namd script present in the namd directory. I am also attaching configuration files for REMD and normal MD.
For normal MD, simulation is running file with the same force field file. Can anyone please tell me how to solve this problem.
Thanks in advance.
Best,
Kaushik
<ubq_ww_pcv1.conf><replica.conf>
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