[gmx-users] distance restraints and lincs warning

[A.Rampioni]

Hi,

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?

Aldo


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 
>>beta-sheet 
>> configuration 1 nm far apart in a truncated octahedron 
>>box.
>> I imposed on both the trimers improper dihedral 
>>restraints on one 
>> peptide and distance restraints among the peptides of 
>>the trimer.
>> I want to bring the two trimers close together, so I 
>>imposed some 
>> distance restraints even between the trimers.
>> 
>> I have performed an energy minimization of the starting 
>>configuration 
>> and a further mdrun with position restraints (without 
>>distance 
>> restraints) for  10 ps.
>> 
>> Then I turn on distance restraints and WITH THE VERSION 
>>3.1.4 EVERYTHING 
>> 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?
> 
> 
> -- 
> Groetjes,
> 
> Anton
> 
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