Please give some suggestions.
Thanking You
---------- Forwarded message ---------
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
Date: Mon, Oct 9, 2023 at 2:39 PM
Subject: Constant pH REMD at explicit solvent
To: AMBER Mailing List <amber.ambermd.org>
Dear Experts,
For constant pH REMD, I follow the tutorials:
http://jswails.wikidot.com/ph-remd.
I run constant pH REMD in explicit solvent. I have 12 replicas (pH 4.5 to
10.0 with increment 0.5). Each replica contains a total of 100 ns
production runs. For a 100 ns production run, I perform 50 simulations of 2
ns each. As for the tutorial, I created 12 directories (named 001, 012, ..,
012) for each replica. So, each directory contains 50 cpout and nc files.
For cphstats, I run the following command:
cphstats --fix-remd prod001 ../001/cpout.rep.001 ../002/cpout.rep.001
../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
../009/cpout.rep.001 ../010/cpout.rep.001 ../011/cpout.rep.001
../012/cpout.rep.001
But for reconstructing pH-based mdcrd files, I do the following steps.
parm amber18.prmtop
trajin ../001/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../002/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../003/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../004/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../005/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../006/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../007/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../008/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../009/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../010/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../011/nc.rep.001 remdtraj remdtrajtemp 7.0
trajin ../012/nc.rep.001 remdtraj remdtrajtemp 7.0
trajout ph7.nc netcdf
go
Are these steps correct?
How can I confirm that "ph7.nc" contains only ph 7 data trajectory?
Thanking You
With regards
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Oct 09 2023 - 11:30:02 PDT
