Dear all,
I'm trying to run constant pH simulation with explicit solvent using
pmemd.cuda. The problem is that the pmemd.cuda is not recognizing the cpin
input file. I have sent a query earlier for help but didn't get any
response. Today I suddenly checked the command line arguments of
pmemd.cuda. It's so surprising that there are no input arguments for CPIN
files.
$ pmemd.cuda --help
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo
-l logfile]
[-amd amdlog_name -gamd gamdlog_name -scaledMD
scaledMDlog_name -suffix output_files_suffix]
I wonder how the CpHMD calculations are done using PMEMD.CUDA. I request
the AMBER experts to kindly look into the matter and help me to find a way
out.
My example script for heating step is as follows:
#!/bin/sh
$AMBERHOME/bin/pmemd.cuda -O \
-i t1.heating.in \
-p t1.parm7 \
-c t1.min.rst7 \
-ref t1.min.rst7 \
-cpin t1.cpin \
-o t1.heating.out \
-cpout t1.heating.cpout \
-r t1.heating.rst7 \
-cprestrt t1.heating.cpin \
-x t1.heating.crd \
-inf t1.heating.info
Thanks,
Bharat Manna
PhD Scholar
IIT kharagpur
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Received on Mon Jul 09 2018 - 04:00:02 PDT
