Hi, Chunli
It just came into my mind that since string method and REMD are separate
code blocks in
pmemd, it seems there is no conflict between them. So you can try with
REMD, but I am not
sure the run will go well.
And you can only set the REMD frequency so that the exchange may only
happen during the
release period of string method(no restraint added). If there is restraint,
the REMD will go wrong.
Feng
On Wed, Aug 2, 2017 at 6:18 PM, Feng Pan <fpan3.ncsu.edu> wrote:
> Hi, Chunli
>
> You can only set -rem to 0, so basically we cannot do REMD for string
> method right now.
>
> Feng
>
> On Wed, Aug 2, 2017 at 5:49 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
>
>> Hellow,
>>
>> Could anyone tell me which value of -rem flags I can specify in string
>> method with swarms of trajectories below:
>>
>>
>> -O -rem 0 -remlog rem.log -i 00.in -o remd.mdout.00 -c 00.rst -r
>> remd.rst.00 -x remd.mdcrd.00 -inf remd.mdinfo.00 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 01.in -o remd.mdout.01 -c 01.rst -r
>> remd.rst.01 -x remd.mdcrd.01 -inf remd.mdinfo.01 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 02.in -o remd.mdout.02 -c 02.rst -r
>> remd.rst.02 -x remd.mdcrd.02 -inf remd.mdinfo.02 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 03.in -o remd.mdout.03 -c 03.rst -r
>> remd.rst.03 -x remd.mdcrd.03 -inf remd.mdinfo.03 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 04.in -o remd.mdout.04 -c 04.rst -r
>> remd.rst.04 -x remd.mdcrd.04 -inf remd.mdinfo.04 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 05.in -o remd.mdout.05 -c 05.rst -r
>> remd.rst.05 -x remd.mdcrd.05 -inf remd.mdinfo.05 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 06.in -o remd.mdout.06 -c 06.rst -r
>> remd.rst.06 -x remd.mdcrd.06 -inf remd.mdinfo.06 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 07.in -o remd.mdout.07 -c 07.rst -r
>> remd.rst.07 -x remd.mdcrd.07 -inf remd.mdinfo.07 -p dna.top
>>
>> -O -rem 0 -remlog rem.log -i 08.in -o remd.mdout.08 -c 08.rst -r
>> remd.rst.08 -x remd.mdcrd.08 -inf remd.mdinfo.08 -p dna.top
>>
>> I checked amber manual:
>>
>> *-rem <#> *This flag defines the type of replica exchange that will be run
>> for 1-D REMD. The allowed values are 1 (T-REMD), 3 (H-REMD), and 4
>> (pH-REMD).
>>
>> Thanks,
>>
>>
>> Best,
>>
>>
>> *Chunli*
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed Aug 02 2017 - 15:30:03 PDT
