[gmx-users] LINCS WARNING...

Anton Feenstra feenstra at chem.vu.nl
Thu Jul 31 09:06:10 CEST 2003

Dallas Warren wrote:
>> I had tried all-bonds and also tried the SHAKE algorithm earlier. They
>> all seem to crash and the culprit always seems to be that one particular
>> hydrogen atom. Is there any other way to make it stable?
> As suggest by David, I would first look at a nearby 1-4 interaction that 
> is too strong.
> Another option is to slow down the hydrogen atoms motion by increasing 
> its mass by a factor of 4 and then subtracting that "extra" mass off the 
> atom it is attached to.  But that isn't likely to help if there is a 
> strong 1-4 interaction happening that is distorting things too much.

The gist of this all is, first look for a 'pathological' cause, e.g. an
error or omission in the topology. Then look for a 'physical' cause, like
big charge interactions, steric clashes and the like. If you are convinced
that isn't going to help, try the tricks.

I can add another possible trick to try. You could turn the hydrogen into
a dummy atom, by shifting its mass to the bonded heavy atom, and defining
one of the [ dummies* ] interactions. See the manual, there are two sections
about it, one under 'Forcefields' and one under 'File formats' (or similar).
If your hydrogen is part of e.g. a hydroxyl, and it needs to be able to
rotate, this won't work (dummies can't rotate like that), but you could
still add an angle constraing manually, by making one additional bond of
the appropriate length. E.g. for a C-O-H hydroxyl, in addition to the C-O
and O-H bonds that are already there, you add a C-H bond of about 0.22nm.
Lincs is able to handle that.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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