[gmx-users] distance restraints and lincs warning
A.Rampioni at rug.nl
Thu Jun 23 12:26:47 CEST 2005
I found the error! I used distance restraints between two
trimers. For some distance restraints it was smaller the
distance between one trimer and the other, while for
others it was smaller the distance between one trimer and
the image of the other. So there were competitive forces
that made explode the box.
Perhaps the interactions with the images are treated in a
different way in the two version 3.1.4 and 3.2.1, so in
one case it gave me an error and in the other not.
Please, if one of the developer can confirm this
interpretation, it would be nice: is that true that in the
two version 3.2.1 and 3.1.4 the interaction between the
system and his images are treated in a different way?
On Tue, 21 Jun 2005 17:48:28 +0200
Anton Feenstra <feenstra at few.vu.nl> wrote:
> A.Rampioni wrote:
>> Dear colleagues,
>> I am performing some simulations on the following
>>system: 3 peptide in a
>> beta-sheet configuration + other 3 peptides in a
>> configuration 1 nm far apart in a truncated octahedron
>> I imposed on both the trimers improper dihedral
>>restraints on one
>> peptide and distance restraints among the peptides of
>> I want to bring the two trimers close together, so I
>> distance restraints even between the trimers.
>> I have performed an energy minimization of the starting
>> and a further mdrun with position restraints (without
>> restraints) for 10 ps.
>> Then I turn on distance restraints and WITH THE VERSION
>> WORKS, BUT WITH THE VERSION 3.2.1 IT DOES NOT WORK !!!
>> Any idea of what can be wrong?
> Have you compared different energies (LJ, Coul, disre,
>etc.) between the versions?
> * NOTE: New Phone & Fax numbers (below) *
> | |
> | _ _ ___,| K. Anton Feenstra
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije
>Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam -
> | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59
> | | Feenstra at few.vu.nl -
> | | "If You See Me Getting High, Knock Me
>Down" (RHCP) |
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list.
>Use the www interface or send it to
>gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users