[gmx-developers] Position-dependent tabulated nonbonded potential tables for a single energy group pair
hess at kth.se
Wed Mar 28 09:07:23 CEST 2012
Using two different potentials will cause all kinds of trouble, as you
will have jumps
in the potential when a particle moves from one region to the other.
If you want to do something like this you have to come up with a potential
which depends continuously on the distance and z-coordinates of the two
You could implement this in the generic non-bonded kernel.
On 03/28/2012 01:33 AM, Beste Bayramoglu wrote:
> Thanks for your response Anton!
> The reason that I want to use different potentials for the same pairs
> in different regions is that because they are in different
> environments when they are in different regions. I cannot use the same
> potentials for all the environments they are in, so that's why I
> should modify the code such that it assigns a specific potential table
> for, let's say 0<box_z<2nm, and then another one for the rest of the
> simulation box_z (for the same energy group pair, of course).
> Any comment from anyone is appreciated.
> On Tue, Mar 27, 2012 at 5:05 AM, Anton Feenstra <k.a.feenstra at vu.nl
> <mailto:k.a.feenstra at vu.nl>> wrote:
> On 27/03/12 10:30, Beste Bayramoglu wrote:
> I've been performing molecular dynamics simulations using
> potentials with Gromacs version 4.0.7. Everything works fine
> with one
> tabulated potential table for each type of energy group pair.
> what I need to do now is that I need to use multiple
> nonbonded potentials (in tabulated form) for each of my energy
> pairs.That's to say, for a certain energy group pair, I need
> to assign
> multiple tables and the program should decide on which one to
> use in the
> calculations depending on the positions of the atoms along
> was wondering if any unofficial attempts to modify the source
> code have
> been made so far for a similar purpose. And which part of the code
> should be changed? I checked the mail list archives, but could
> not find
> such an entry. I know that this is going to be a very
> difficult task for
> a newbie like me and probably would take quite some time, so
> I'd like to
> know beforehand if what I want to do is reasonable.
> Unfortunately, I
> don't have much time until I graduate, so if it's not
> reasonable I'd
> have to think about other alternatives. I would really
> appreciate if
> anyone could help me with this.
> This sounds very complicated.
> It would be good if you could explain what it is that you want to
> achieve with these interactions?
> That way you may benefit from the combined expertise of the list
> members in finding a workable solution for your problem.
> _____________ _______________________________________________________
> | |
> | _ _ ___,| K. Anton Feenstra
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