[gmx-users] warning: 1-4
feenstra at chem.vu.nl
Mon Aug 30 08:08:47 CEST 2004
> Hello, dr. gmx-users,
> My MD simulation of protein and ligand end with warning:
> 1-4 interactions between 83 and 86 at distance larger than 2 nm.
> Soon it ends with segmentation foult.
> I did EM and partial MD (constrains = all-bonds for ~ 500 ps).
> everything was OK'. I cheked that 83 and 86 atoms belong to Ser
> residue and CA and HG atoms of my protein, so topologies are fine (i
> Have no idea what's wrong.
You shoulc check for bad contacts in and around these atoms, in your
starting structure as well as the last conformation before the crash.
(mdrun probably wrote a pair of 'step-*.pdb' files, one of the step at
which the crash occurred, and one of the step before that.)
If that doesn't help, check the energy components (bonds, angles, dih's,
idih's, coul, vdw) and see if any goes up steeply before the crash.
| | |
| _ _ ___,| 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" |
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