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

Asaf Farhi asaf.farhi at weizmann.ac.il
Wed Mar 28 18:44:37 CEST 2012

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.
if (V>cutoff)
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,

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

> 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!

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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