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

[Thomas Piggot]

If this is the case then I think you have to take David's advice and you 
will have to patch openmm to get it to do what you want. Or I suppose 
decide if you really need to use mdrun-openmm rather than normal mdrun.

Tom

Hans HEINDL wrote:
> 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.
>>
> 
> 

-- 
Thomas Piggot
University of Bristol, UK.