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

[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.