Hi,
> After running, It generates 12 trajectory file names as p1.crd.0, ..p1.crd.11.
> But p1.crd.0 contains different pH coordinates, not a single pH coordinate.
Yes, because that's what you asked cpptraj to do. Your input was:
ensemble ../001/nc.rep.001 trajnames <list> remlog ../rem.001.log
nstlim 1000 ntwx 1000
The 'ensemble' command entry of the cpptraj manual explains what the
'remlog' keyword does:
"[remlog <remlogfile>] For H-REMD trajectories only, use specified
REMD log file to sort trajectories by coordinate index (instead of by
replica/Hamiltonian)."
It's really important to read the manual entry for the
commands/keywords you are using so you can be certain you know what
they are doing. If you want things sorted by Hamiltonian (in this case
pH) just remove the remlog/nstlim/ntwx keywords.
-Dan
On Tue, Oct 10, 2023 at 3:02 PM Dulal Mondal
<babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
> Thank You, sir, for your reply.
>
> I have some queries about the ensemble command.
>
> parm ../amber18.prmtop
>
> ensemble ../001/nc.rep.001 trajnames ../002/nc.rep.001,../003/nc.rep.001,../004/nc.rep.001,../005/nc.rep.001,../006/nc.rep.001,../007/nc.rep.001,../008/nc.rep.001,../009/nc.rep.001,../010/nc.rep.001,../011/nc.rep.001,../012/nc.rep.001 remlog ../rem.001.log nstlim 1000 ntwx 1000
>
> trajout p1.crd remdtraj
> go
>
> After running, It generates 12 trajectory file names as p1.crd.0, ..p1.crd.11.
> But p1.crd.0 contains different pH coordinates, not a single pH coordinate.
> But In cpptraj manual https://amberhub.chpc.utah.edu/ensemble/
>
> parm ala2.99sb.mbondi2.parm7
> ensemble rem.crd.000 trajnames rem.crd.001,rem.crd.002,rem.crd.003
> trajout temp.crd
> distance d1 out d1.ensemble.dat @1 @21
>
> This will output 4 temperature trajectories named ’temp.crd.X’, where X ranges from 0 to 3 with 0 corresponding to the lowest temperature, and ’d1.ensemble.dat’ containing 4 columns, each corresponding to a temperature.
>
>
>
> On Tue, Oct 10, 2023 at 6:39 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> 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.*
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> With regards,
> Dulal Mondal,
> Research Scholar,
> Department of Chemistry,
> IIT Kharagpur, Kharagpur 721302.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 11 2023 - 06:30:02 PDT
