[gmx-users] Disabling the pair-list update in REMD

Mateusz Marianski marianski at fhi-berlin.mpg.de
Fri Apr 17 15:07:05 CEST 2015

Hi Mark,

Thank You for the prompt answer. It clarified a lot and guided me to the 
place where the switch for replica-exchange initiated neighbor search is 
encoded.  I have it running now.


On 04/16/2015 06:42 PM, Mark Abraham wrote:
> On Thu, Apr 16, 2015 at 5:18 PM, Mateusz Marianski <
> marianski at fhi-berlin.mpg.de> wrote:
>> Hi all,
>> I am trying to circumvent  the update of the list of neighbor atoms for
>> which the long-range interactions in Cutoff scheme are evaluated. In
>> essence, I want to maintain the initial neighbor-list for long-range
>> interaction for whole simulations. In a simple MD run setting the nstlist
>> parameter to 0 will prohibit the update of the list.
>> Nevertheless, when I try remd, it does not work anymore, since - as it
>> states in the manual:
>> "The velocities are scaled and neighbor searching is performed after every
>> exchange."
>> Is there any way to disable the neighbor-search performed during the
>> exchange of replicas?
> No. GROMACS exchanges the coordinates (unlike various other MD packages, I
> understand), and does not exchange the neighbour-search data structures,
> which thus requires the latter to be rebuilt. One could turn that off, thus
> using the neighbour-search structure originally built for whichever replica
> was in the destination ensemble, but that sounds pretty crazy (e.g. solvent
> diffusing differently in every replica). But maybe you have that sorted,
> somehow? It would not be all that hard to rework to swap the ensemble data
> instead of the coordinates, but getting that right for all possible
> algorithm and integrator combinations doesn't sound like fun...
> Mark
>> PS. Yes, I am aware of all potential flaws/problems with not updating the
>> neighbor-list in simulations. It's (hopefully) under control :).
>> Best,
>> Mateusz
>> --
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.

Mateusz Marianski, PhD
email:          marianski at fhi-berlin.mpg.de
phone:                     +49-30-8413-4849
der Max-Planck-Gesellschaft
Faradayweg 4-6
14195 Berlin, Germany

More information about the gromacs.org_gmx-users mailing list