> I'm concerned about the steric clashes throwing the energetics of my system
> off-course. What if I try to minimize my system in vacuum beforehand?
Of course, you can try this... Also, sometimes if atoms are overlapped
(within their vdw sphere) and of opposite charge, you can cause molecular
mechanics nuclear fusion. Use ptraj and the checkoverlap command:
ptraj prmtop << EOF
checkoverlap
EOF
If you see lot's of close contacts, what I have done in the past is to
minimize first with electrostatics turned off...
&cntrl
nmropt=1,
imin=1, maxcyc = 500, ncyc = 500,
&end
&wt
type='ELEC', value1 = 0.0,
&end
&wt
type='END',
&end
&rst iat = 0, &end
Note that the electrostatics will not be exactly zero, but this will
remove overlaps often sufficiently for continuing (however overlaps could
be symptoms of a deeper problem in the setup of the initial coordinates).
-- tec3
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Received on Wed Mar 05 2008 - 06:07:38 PST
