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

[Anton Feenstra]

I suppose you might then use the free-energy code and create a 
z-dependent lambda.

But you haven't yet explained what you want to achieve - what kind of 
system is this that you need this kind of interactions?

On 28/03/12 09:07, Berk Hess wrote:
> 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
> particles.
> You could implement this in the generic non-bonded kernel.
>
> Cheers,
>
> Berk
>
> 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.
>>
>> Thanks,
>>
>> Beste
>>
>> 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:
>>
>>         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
>>     _____________ _______________________________________________________
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>>     | _ _ ___,| K. Anton Feenstra |
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>>
>>
>>
>>
>


-- 
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)      |
|_____________|_______________________________________________________|