[gmx-developers] Position-dependent tabulated nonbonded potential tables for a single energy group pair

[Beste Bayramoglu]

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.

Thanks,

Beste

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:
>
>> Hi,
>>
>> 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.
>
>
> --
> Groetjes,
>
> Anton
>  _____________ ______________________________**_________________________
> |             |                                                       |
> |  _   _  ___,| 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...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20120327/09048a07/attachment.html>