[gmx-developers] FW: Questions - cutoff in the bondingpotentialand editing the replica exchange function

[Shirts, Michael (mrs5pt)]

Hamiltonian replica exchange is planned for 4.6, so you might want to wait
for that to come out.

It's still very unclear what you want to do with the truncated potentials,
and it's unlikely you'll get anyone to help you if you can't make it clear.
It sounds like you might be implementing something like this
http://dx.doi.org/10.1002/jcc.21938?

But very hard to tell.  The tabulated potentials are likely to be the best
things to start with.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Asaf Farhi <asaf.farhi at weizmann.ac.il>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Wed, 28 Mar 2012 22:19:12 +0000
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: RE: [gmx-developers] FW: Questions - cutoff in the
> bondingpotentialand editing the replica exchange function
> 
> Dear Christoph
> 
> Thank you very much for the reply.
> Cutoff in the energy per pair would be good. How is tabulating done?
> About the replica exchange. Most of the chances I'll need to change it. It's
> something similar to H-REMD and I can send you the details as soon as I get to
> the office.
> 
> Thanks again,
> Best regards,
> Asaf
> 
> ________________________________________
> From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org]
> on behalf of Christoph Junghans [junghans at votca.org]
> Sent: Wednesday, March 28, 2012 8:00 PM
> To: Discussion list for GROMACS development
> Subject: Re: [gmx-developers] FW: Questions - cutoff in the
> bondingpotentialand editing the replica exchange function
> 
> Hi Asaf,
> 
> Am 28. März 2012 10:44 schrieb Asaf Farhi <asaf.farhi at weizmann.ac.il>:
>> Dear Professor Shirts
>> 
>> Thank you very much for the reply.
>> I thought about it more. It will also be good for us to use cutoff in the
>> energy. This cutoff is for the maximal energy (for the nonbonded
>> interactions).
>> Editing the RE function might be unnecessary (Another way of implementation).
>> In other words what is needed is to use cutoff for the energy so it won't be
>> larger than a certain value (total VDW and electrostatic) and this value
>> should be constant for all pairs.
>> e.g
>> if (V>cutoff)
>>  V=cutoff;
> I am not sure, do you want to cutoff the total bonded energy or just
> the energy per pair (interaction function)? The latter can easily be
> done by tabulating the bonded interaction.
> 
> And what do you want to change about the replica exchange function?
> 
> Cheers,
> 
> Christoph
> 
>> Using cutoff in the bonding energy can also be used but it seems complicated
>> and I'm not sure necessary.
>> Another small thing is if you know if you can exclude certain atoms from the
>> non bonded interactions?
>> Could you help us with that?
>> 
>> Many thanks,
>> best regards,
>> Asaf
>> 
>> 
>> ________________________________________
>> From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org]
>> on behalf of Shirts, Michael (mrs5pt) [mrs5pt at eservices.virginia.edu]
>> Sent: Tuesday, March 27, 2012 3:50 PM
>> To: Discussion list for GROMACS development
>> Subject: Re: [gmx-developers] FW: Questions - cutoff in the bondingpotential
>> and editing the replica exchange function
>> 
>> Hi, Asaf-
>> 
>> I think you need to be more specific to get any useful response.
>> 
>>> One is about how to add cutoff to the bonding energy (I guess the pairing
>>> terms can be done without editing the code)
>> 
>> It's not clear what the purpose of adding a cutoff to the bonded term would
>> be.
>> 
>>> and the other one is if anyone
>>> wants to help us in editing the replica exchange function (cooperation)?
>> 
>> You need to specify what you are editing it to do!
>> 
>> Best,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821
>> 
>> 
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> 
> 
> 
> --
> Christoph Junghans
> Web: http://www.compphys.de
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