I have fixed and checked in the even-number replica problem for H-REMD back
a few months ago...but not T-REMD. It is pretty trivial but I currently
don't have time to do the tests/QC work...
If anyone is interested to do T-REMD part, just take a look at the H-REMD
part.
Taisung
-----Original Message-----
From: Adrian Roitberg [mailto:roitberg.ufl.edu]
Sent: Wednesday, September 25, 2019 12:15 PM
To: amber-developers.ambermd.org
Subject: Re: [AMBER-Developers] requirement for an even number of replicas
in replica exchange?
Just to add one potential issue, I am going to guess that the calculations
for the remlog files makes the implicit assumption of an even number of
replicas, so there is a certain symmetry on how it is computed and when.
On 9/25/19 6:11 PM, koushik kasavajhala wrote:
> EXTERNAL EMAIL: Exercise caution with links and attachments.
>
>
>
>
> To add to what Carlos has said, the main problem might arise during
> mpi_send() and mpi_recv() calls. Currently, different variables are
> sent and received during REMD using the MPI protocols. I am not sure
> how these would work when odd number of replicas/processors are used.
> Maybe others might know how to overcome this. In terms of doing the
> exchange calculation itself, it should be trivial to perform with odd
number of replicas.
>
> On Wed, Sep 25, 2019 at 11:38 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> I think conceptually it isn't hard. An easy way would be to alternate
>> having the first or last replica not involved in exchanges, leaving
>> an even number to pair for exchange. Right now the first/last attempt
>> exchange on alternate attempts, which usually fails, so having one of
>> them do nothing every other time would be similar. The bookkeeping
>> would need to be updated for things that assume even numbers, and
>> selection of partners is a little more complicated, but I think it
>> should work without too much rewriting. It was always easier to code
>> with even numbers, and an extra replica didn't seem to cost much so we
did it that way.
>> Others might know of specific issues in the current code that would
>> be difficult to change...
>> carlos
>>
>> On Wed, Sep 25, 2019, 10:12 AM David Case <david.case.rutgers.edu> wrote:
>>
>>> Does anyone have a feeling of how easy/hard it would be allow an odd
>>> number of replicas in (Hamiltonian) replica exchange?
>>>
>>> ...thx...dac
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.or
>>> g_mailman_listinfo_amber-2Ddevelopers&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvc
>>> nVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=S8rdcFK1FgzpZ7WIYFSTuIzsIOkaDJo16y7Jv
>>> JS-Kdg&s=dPiVtqau5S97iNveeOFcdASg7prAoO2qcFKFhhf_N8o&e=
>>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org
>> _mailman_listinfo_amber-2Ddevelopers&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnV
>> g&r=dl7Zd5Rzbdvo14I2ndQf4w&m=S8rdcFK1FgzpZ7WIYFSTuIzsIOkaDJo16y7JvJS-
>> Kdg&s=dPiVtqau5S97iNveeOFcdASg7prAoO2qcFKFhhf_N8o&e=
>>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_
> mailman_listinfo_amber-2Ddevelopers&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&
> r=dl7Zd5Rzbdvo14I2ndQf4w&m=S8rdcFK1FgzpZ7WIYFSTuIzsIOkaDJo16y7JvJS-Kdg
> &s=dPiVtqau5S97iNveeOFcdASg7prAoO2qcFKFhhf_N8o&e=
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor Department of Chemistry
University of Florida roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Wed Sep 25 2019 - 12:00:02 PDT
