[gmx-developers] Re: seg fault with distance restraints - problem in graph

[Anton Feenstra]

Michael Shirts wrote:

> So, I've investigated this a little more.
> 
> The problem appears to be that distance restraints (and bond type=6) are set
> up NOT to make chemical bonds.  However, when the fshift is calculated,
> (around line 330 in disre.c, version 3.1.4) it uses the molecular graph, which
> does not take the distance restraints or bonds type=6 into account.
> 
> This appears to mean that distance restraints will not work between two atoms
> that are otherwise unconnected -- if they are connected by SOME other series
> of bonds, it should work OK (or perhaps there are other situations it will
> break down as well).  If they are not connected EXCEPT by the distance
> restraint (or by bond type=6), when fshift is computed, it will gad.
> 
> Any thoughts?  Is this a bug that needs to  be fixed?

There are a number of flags for interaction functions, the one you mention
for 'chemical bonds' is one. There is another that sets 'connect', which is,
IIRC, what should be used for PBC handling (i.e. for fshift).
Check if this is set for disres, and for bonds type=6 while you're at it...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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