[gmx-developers] Position-dependent tabulated nonbonded potential tables for a single energy group pair
bbayramoglu at ucdavis.edu
Wed Mar 28 01:33:19 CEST 2012
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> wrote:
> On 27/03/12 10:30, Beste Bayramoglu wrote:
>> I’ve been performing molecular dynamics simulations using tabulated
>> potentials with Gromacs version 4.0.7. Everything works fine with one
>> tabulated potential table for each type of energy group pair. However,
>> what I need to do now is that I need to use multiple position-dependent
>> nonbonded potentials (in tabulated form) for each of my energy group
>> 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 z-direction.I
>> 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 |
> | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
> |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
> | | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
> | | "Carbohydrates is all they groove" (Frank Zappa) |
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-developers