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

TJ Piggot t.piggot at bristol.ac.uk
Thu Jan 7 00:15:00 CET 2010

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.


------------ 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>
Subject: simulationg a distance restraint with a type 6 bond in gromacs


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

University of Westminster UK

---------- End Forwarded Message ----------

TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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