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

Daniele Bemporad DANIELE at biop.ox.ac.uk
Tue Aug 5 19:17:47 CEST 2003

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.

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.

Thanks a lot

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