On 10/11/23 9:46 AM, Dulal Mondal via AMBER wrote:
> [External Email]
>
> Dear Sir,
> Thank You, sir, for your reply.
>
> I understand my mistake.
>
> But after running the ensemble command, it generates 12 trajectory files
> named p1.crd.0, ..p1.crd.11.
> p1.crd.0 > pH 4.5
> ..
> p1.crd.11> pH 10.0
>
> But each trajectory file contains the same number of frames. How Is that
> possible?
> Because no. of frames at a particular pH depends on the exchange
> probability.
No, its does not!
The total numbers of frames per replica must be exactly the same, as is
the number of frames per pH. Think about this. Everytime you do an
exchange, you move one structure from the replica at pH_i to Ph_J and
ONE structure from pH_j to pH_i, so the total number at each pH is
conserved.
Adrian
>
> On Wed, Oct 11, 2023 at 6:56 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> 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.
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Oct 11 2023 - 09:00:03 PDT
