[gmx-users] criticism invited...

[Paul Barrett]

It happens every time, normally within about 300ps of restraint
removal.

Thanks to everyone for a great set of suggestions.

Paul

>Christoph Freudenberger wrote:
>> Paul Barrett wrote:
>> 
>>> My (alledged) solution: combine this hydrogen with its neighbouring
>>> oxygen by:
>[...]
>> I cannot judge how much this will effect the results in your special case,
>> but i don't think it's "good force field practice".
>
>I would tend to agree with that.
>
>> I would try to add the hydrogens mass into the oxygen
>> and define the hydrogen as a dummy keeping it's charge
>> and LJ's.
>
>Can't have a rotatable dummy, though. Try the addition of
>a dihedral angle potential David suggested, and/or shift
>mass from the oxygen to the hydrogen.
>
>Do you get this spinning OH group repeatedly? If it only
>happens eveery once in a while, you can use my 'upstream
>tweaking': write a .trr frame in slightly reduced precision
>(e.g. 6 in stead of 7 decimal places), and continue the
>run with that. I;ve posted a more complete description on
>the list only several days back.
>
>
>-- 
>Groetjes,
>
>Anton
>  _____________ _______________________________________________________
>|             |                                                       |
>|  _   _  ___,| K. Anton Feenstra                                     |
>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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>| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
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