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

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 1 00:57:09 CEST 2012 

On 31/03/2012 7:26 PM, Asaf Farhi wrote:
> Dear Mark
> Thank you very much for the reply!
> I read 6.7, about coulombtype =Cut-off, and wanted to ask if it means:
>
> if (V<Ecutoff)
>     V=0;
> or
> if (V>Ecutoff)
>     V=Ecutoff;
>
> I need the second one and I didn't manage to understand which one is it.

The first one is implemented, though it is usually phrased as (r > 
r_cutoff) => (V=0), since a Coulomb potential has V->0 as r->inf. You 
have to use some kind of a cut-off, as the number of interactions you 
have to compute grows with dvolume/d(r_cutoff), i.e. as (r_cutoff)^2.

For normal MD the value of V at any point is irrelevant, because only 
the forces appear in the equations of motion. The value of (some 
components of) V might appear in the RE equations, but only if they 
don't cancel out for candidate exchange pairs in the subtraction of the 
exchange test does the value of V past the cutoff become relevant.

Mark

>
> Thanks in advance,
> Best regards,
> Asaf
> ________________________________________
> From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
> Sent: Saturday, March 31, 2012 1:36 AM
> To: Discussion list for GROMACS development
> Subject: Re: [gmx-developers] FW: Questions - cutoff in thebondingpotentialandediting the replica exchange function
>
> On 31/03/2012 4:49 AM, Asaf Farhi wrote:
>> Dear Cristoph
>>
>> Thank you very much for the reply.
>> I looked at 4.2.13 and it seems that the bonds and angles terms can be edited. Do you know how can one edit the potentials between unbonded atoms (VDW and electrostatic)
> Tabulated nonbonded interactions. Manual 6.7.
>
>> I need the same cutoff for all the interactions.
> Easily done already.
>
> Mark
>
>> About the replica exchange I need it to be H-REMD (constraints and bonding potentials maybe don't need to be multiplied by lambda).
>> I still haven't been to the office (I was in a trip).
>> Does anyone know when will the new version of GROMACS be released? Alternatively is someone willing to cooperate with us on that?
>> I'll send all the material if anyone considers it.
>>
>> Thanks in advance,
>> Have a good weekend,
>> Asaf
>>
>>
>> ________________________________________
>> From: gmx-developers-bounces at gromacs.org [gmx-developers-bounces at gromacs.org] on behalf of Christoph Junghans [junghans at votca.org]
>> Sent: Thursday, March 29, 2012 12:45 AM
>> To: Discussion list for GROMACS development
>> Subject: Re: [gmx-developers] FW: Questions - cutoff in thebondingpotentialand editing the replica exchange function
>>
>> Am 28. März 2012 16:19 schrieb Asaf Farhi<asaf.farhi at weizmann.ac.il>:
>>> Dear Christoph
>>>
>>> Thank you very much for the reply.
>>> Cutoff in the energy per pair would be good. How is tabulating done?
>> See manual section 4.2.13 and the gmx-users mailings list.
>>
>>> 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.
>> The place to look for the exchange rates is the function
>> get_replica_exchange inside src/kernel/repl_ex.c
>>
>> Christoph
>>> 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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>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
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