On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:
[ dihedral_restraints ]
; ai aj ak
al type label phi dphi kfac power
; phi C'(n-1) - N - CA - C'
3
5 7 8 1 1 -90 75 2 1
Try mdrun -debug on a short run. What does it have to say about the
parameter values for this dihedral restraint? Likewise gmxdump -s on
the .tpr (though you will have to search around for F_DIHRES among
other things, probably).
I have run a 500 ps run with -debug on, but I am unsure of where
should I look for what it says of relevance -I see the ctab,rtab,dtab
xvg's but I doubt they are of interest.
There should be a much larger .log file, probably named differently.
Check what it reports about dihedral restraints - text searching will be
your friend, here.
Found - mdrun0.log . It's a 4.2 Gb file (argh), I am now trying to grep
it and see.
m.
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