[AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda?

From: Bharat Manna <bharatmanna.gmail.com>
Date: Mon, 9 Jul 2018 16:01:39 +0530

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

$ 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

My example script for heating step is as follows:


$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


Bharat Manna
PhD Scholar
IIT kharagpur
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Received on Mon Jul 09 2018 - 04:00:02 PDT
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