# [gmx-developers] FW: Questions - cutoff inthebondingpotentialandediting the replica exchange function

Asaf Farhi asaf.farhi at weizmann.ac.il
Sun Apr 1 10:41:14 CEST 2012

```Dear Mark

Thank you very much for the reply!
Do you know how can I change the potential so it'll be the second one (or the forces)?
If it can't be done by the user is anyone willing to help us with that?

Thanks again,
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: Sunday, April 01, 2012 1:57 AM
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] FW: Questions - cutoff inthebondingpotentialandediting the replica exchange function

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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