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

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Mon, 9 Jul 2018 11:58:23 +0000

Hi Bharat,


Which version of pmemd.cuda are you using?

Someone can correct me if I am wrong but CpHMD has only been implemented in Amber16 (Amber14 at the very best). This might explain the error you are having...


Best,


Eric 


--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
________________________________
From: Bharat Manna <bharatmanna.gmail.com>
Sent: 09 July 2018 11:31
To: amber.ambermd.org
Subject: [AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda?
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 - 05:00:01 PDT
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