[AMBER] Need help regarding Constant pH MD in pmemd.cuda

From: Bharat Manna <bharatmanna.gmail.com>
Date: Fri, 6 Jul 2018 12:07:08 +0530

Dear all,

I'm trying to run constant pH simulation with explicit solvent using
pmemd.cuda. 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

The problem is that the pmemd.cuda is not recognizing the cpin input file
and no cpout or cprestrt files are generated. All the minimization, heating
and equilibration steps are running with no error message and producing the
other files. However, same inputs are running fine in SANDER.MPI and I am
getting the cpout or cprestrt files. Please help me to troubleshoot the

Bharat Manna
PhD Scholar
IIT Kharagpur
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Received on Fri Jul 06 2018 - 00:00:02 PDT
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