From: Alao, John-Paul (alaooj_at_miamioh.edu)
Date: Mon Nov 09 2020 - 11:01:26 CST
Dear mailing list,
I generated the configuration files to run absolute protein-ligand binding
free energy using Charmm-GUI. However, this part of the code crashes.
# FEP/λ-REMD Simulation, Runing 4 ns (200 ps x 20)
cnt=0
cntmax=20
while [ ${cnt} -le ${cntmax} ]
do
if [ ${cnt} -eq 0 ]
then
charmrun /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24
+replicas 24 fep_${system}.conf --source FEP_remd_softcore.namd +stdout
output_${system}/%d/job${cnt}.%d.log
else
charmrun /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24
+replicas 24 restart_${cnt}.conf --source FEP_remd_softcore.namd +stdout
output_${system}/%d/job${cnt}.%d.log
fi
cnt=$[$cnt+1]
done
*The error message is:*
Running command: /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24
+replicas 24 fep_solv.conf --source FEP_remd_softcore.namd +stdout
output_solv/%d/job0.%d.log
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 24 threads
./fep.sh: line 40: 106230 Segmentation fault (core dumped) charmrun
/software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24 +replicas 24
fep_${system}.conf --source FEP_remd_softcore.namd +stdout
output_${system}/%d/job${cnt}.%d.log
Running command: /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24
+replicas 24 restart_1.conf --source FEP_remd_softcore.namd +stdout
output_solv/%d/job1.%d.log
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 24 threads
./fep.sh: line 40: 106232 Segmentation fault (core dumped) charmrun
/software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24 +replicas 24
restart_${cnt}.conf --source FEP_remd_softcore.namd +stdout
output_${system}/%d/job${cnt}.%d.log
Please can anyone assist with information on how to get around this? Thanks
a lot.
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:14 CST