Hi all,
I'm trying to run a simulation with a restraint in the production phase. I
understand that you can do this in PMEMD using the old style amber group
specifications. I've set up the infile as follows:
###################
Constant pressure constant temperature production run
&cntrl
nstlim=12500000, dt=0.002, ntx=5, irest=1, ntpr=50, ntwr=5000, ntwx=10,
temp0=300.0, ntt=1, tautp=2.0, iwrap=1, ig=-1
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
ntr=1,
&end
title1
RES 1
END
Weight
WT 10
END
END
#####################
The command I use to run pmemd.MPI is as follows:
mpirun pmemd.MPI -O -i prod.in -o md_1.out -c ../CP/CP.rst -r md_1.rst
-p ../leap/hex_ligand.parm -x md_1.crd -ref ../CP/CP.rst
The -ref option points to the last restart file created in Constant
pressure equilibration and is present. However, I get the error:
| Largest sphere to fit in unit cell has radius = 11.874
Unit 8 Error on OPEN:
Any help you could provide would be greatly appreciated.
Kind regards,
GT
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Received on Tue May 22 2012 - 11:00:03 PDT
