Hi,
First, 'remdtraj remdtrajtemp' is only for T-REMD runs. I think it may
have worked for pH REMD trajectories from older versions of Amber, but
trajectories from more recent versions will cause CPPTRAJ to give you
an error message like "Target replica not found" if you use it for pH
trajectories. The correct usage is:
trajin <file> remdtraj remdtrajvalues <pH>
So you want:
parm amber18.prmtop
trajin ../001/nc.rep.001 remdtraj remdtrajvalues 7.0
trajin ../002/nc.rep.001 remdtraj remdtrajvalues 7.0
...
trajout ph7.nc
Then to confirm ph7.nc has only pH 7 you can extract the remd_values
variable like so:
ncdump -v remd_values ph7.nc
Hope this helps,
-Dan
On Mon, Oct 9, 2023 at 5:10 AM Dulal Mondal via AMBER <amber.ambermd.org> wrote:
>
> 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.*
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Received on Tue Oct 10 2023 - 06:30:03 PDT
