[gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

[Hans HEINDL]

Thanks Tom,

It may easily be that the 6- bond type works in mdrun but not in
mdrun-openmm. This would be an explanation for the ridiculous force
constants

Hans


Am Mittwoch, den 06.01.2010, 23:15 +0000 schrieb TJ Piggot:
> Please keep all correspondence on the GROMACS mailing list, it gives you a 
> much greater chance of someone being able to help you.
> 
> I have used this bond type before and have had no problems (with force 
> constants much smaller than those which you apply). I would make sure that 
> your box is big enough so that this bond is not being applied across the 
> boundary. Otherwise someone else may have more ideas to help you.
> 
> Tom
> 
> ------------ Forwarded Message ------------
> Date: Wednesday, January 06, 2010 22:43:20 +0100
> From: Hans HEINDL <hheindl at terra.es>
> To: TJ Piggot <t.piggot at bristol.ac.uk>
> Cc:
> Subject: simulationg a distance restraint with a type 6 bond in gromacs
> 
> Hi,
> 
> As you remember we discussed simulation of a restraint which is not yet
> implemented in mdrun-openmm by creating a 'bond'. Type 1 bonds did not
> work but the type 6 did the job but I could not restrain the distance at
> the value I projected. The distance between the ends of my peptide
> should remain 57 angstroms and the best I accomplished was holding the
> distance fairly well for a ns and then it broke down to a much smaller
> value. (I tried to define the bond with:
> 
> 1	614	6	 5.761 400000
> 
> with the energy term for the bond length obviously too small. But even
> if I got up to 300 000 000 up to 1 000 000 000 I got no proper result.
> 
> The best results were recieved with
> 
> 1	614	5	5.671	5.671	5.671	5.671
> 
> but even with such an extreme example the distance tended to shrink
> 
> 
> kind regards
> 
> Hans HEINDL	
> University of Westminster UK
> 
> 
> 
> ---------- End Forwarded Message ----------
> 
> 
> 
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>