[gmx-users] cyclic problems...

Henrik Rundgren henrik at physc.su.se
Tue May 11 13:20:47 CEST 2004

Hello, again.
I am running a cyclic peptide, and this warning comes up...

Warning: 1-4 interaction at distance larger than 2.56
These are ignored for the rest of the simulation
turn on -debug for more information
Segmentation fault

First, is this a warning for an interaction at a distance between 2 atoms?
Or is 2 atoms (1-4 to each other) at a distance of  >2.56 Å?

I've looked at the last frames, and it looks ok with ngmx...
With GOP I can see that there is an ackward configurtion right when it 
crashes..or close to it....
I figure that it could have something to do with that..
An angle of 53 degrees between 2 residues, this leads to a  (C)O that 
comes pretty close to an N.... Then the corresponding CB is at a 
distance that is 3.59 Å.....
And a few steps before this fragment -NME and -CO are cis (1.3 Å from 
each other)!?!?

The simulation has been running for 2.2 M steps... so it didn't really 
crash immediately. I use ffG43a2.
Does the problem lie that there where to big forces prior to crash and 
that it "throws away" one atom... and this leads to crash? If so, can I 
get around that, and can the FF bring it back to "normal" conditions?


Henrik Rundgren
Division of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm

E-mail:    Henrik at physc.su.se
Telephone: +46-(0)8-16 12 63
Fax:       +46-(0)8-15 21 87
Website:   www.fos.su.se/~henrik

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