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

[Mark Abraham]

On 29/03/2012 9:19 AM, Asaf Farhi wrote:
> Dear Christoph
>
> Thank you very much for the reply.
> Cutoff in the energy per pair would be good. How is tabulating done?

It seems as though you haven't checked out the manual about tabulated 
interactions (bonded and non-bonded, they're different) nor the use of 
energy group exclusions. It's useless to consider modifying a program 
until you have a basic understanding how it works already.

The contribution of the bonded interactions to the total PE is very 
small, so tabulating them for cut-offs is probably unnecessary or even 
useless. Sometimes you've talked about bonded interactions, and other 
times non-bonded. I still haven't seen a clear single statement of your 
objective, why it might be useful and how you think you might achieve 
it. Please respect the time that other people might give to you :-)

Mark

> 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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