[gmx-developers] -dummy aromatics: problem with TRP

Anton Feenstra feenstra at chem.vu.nl
Wed Aug 6 10:31:10 CEST 2003

Daniele Bemporad wrote:
> Hi all
> Apparently my subscription to gmx-developers does not allow me to post
> gmx-users and I do not feel like subscribing both lists because I would
> probably receive hundreds of emails. So my message is posted here.

You can subscribe to the users list and then turn off e-mail delivery
and check new mail from the list archive. Or have your mail program filter
gmx-users mail into a separate folder. We rather not have user-related
discussions on the dev list, for obvious reasons.

> My problem is that when I use the option "-dummy aromatics" with proteins
> containing the TRP residue, the simulations crash with LINCS errors
> involving the C_alpha-C_beta bond of the TRP residue. This has happened
> at least in 2 different systems of mine, and with various time steps
> (from 1 to 5 fs). From the mailing list, it seems like nobody has reported
> this problem before, but I cannot find any error in my runs. Should I
> keep on looking for possible mistakes in what I do, or has someone
> discovered a little bug and fixed it ? I have seen there are problems
> with dummy atoms when using the new force field, but I'm using the
> original ffgmx force field.

I have seen similar problems occasionally while testing the 'dummy
aromatics' implementation (which I wrote). The problem, I figure, is
that forces from any 'bad' contacts on the rigidified aromatic ring
will be transferred 'wholesale' to the Ca-Cb bond. I.e. there can be
many neighbors pulling and pushing the ring, and since the ring can't
and won't give in, all these forces affect the first non-rigid part:
the Ca-Cb bond.

Things to check first are, does your system run well without dummies,
or with dummy hydrogens only? Have you tried EM with dummies? Do you
use Lincs for constraints? I have never tested the dummy constructions
in combination with Shake, it should also work, but may not. Increasing
Lincs-order (e.g. from 4 to 8), especially during EM, could help
convergence and/or stability (and at minimal computational cost).


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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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