[gmx-developers] Position-dependent tabulated nonbonded potential tables for a single energy group pair
k.a.feenstra at vu.nl
Wed Mar 28 11:00:56 CEST 2012
I suppose you might then use the free-energy code and create a
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
> 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 |
>> | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
>> |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
>> | \_/ \_/ | | | Tel +31 20 59 87783 <tel:%2B31%2020%2059%2087783>
>> - Fax +31 20 59 87653 <tel:%2B31%2020%2059%2087653> - Room P136 |
>> | | Feenstra at few.vu.nl <mailto:Feenstra at few.vu.nl> -
>> www.few.vu.nl/~feenstra/ <http://www.few.vu.nl/%7Efeenstra/> |
>> | | "Carbohydrates is all they groove" (Frank Zappa) |
| | |
| _ _ ___,| 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) |
More information about the gromacs.org_gmx-developers