> I read all the mails that you send me. I tried all the suggestions that
> you advice me when I understand them and try to found a way to check the
> overlap with "checkoverlap" because it is not really explain in the
> manual. I am really sorry if you feel that I don't take time to read
(ptraj or cpptraj)
ptraj prmtop << EOF
trajin inpcrd
checkoverlap
EOF
where prmtop is your prmtop and inpcrd is your initial set of
coordinates.
Also, when I do have overlaps, you can try one or two things...
(1) minimize w/ electrostatics effectively turned off
title
imin = 1, maxcyc = 2500, ncyc = 2500,
ntb = 2,
cut = 9.0,
nmropt = 1, ntpr = 50,
&end
&wt
type = 'ELEC', value1 = 0.0,
&end
&wt
type = 'END',
&end
&rst
iat = 0,
&end
(2) If lot's of overlapping atoms, try scaling the coordinates, then
increase the box size manually in restrt file and then run extensive
constant pressure MD to relax the system. To scale, I think the below
ptraj/cpptraj input would work (but cannot test since our machines are
down today). It would scale by multiplying each coordinate by 1.2
ptraj prmtop << EOF
trajin inpcrd
trajout inpcrd.scaled restrt
scale * x 1.2 y 1.2 z 1.2
EOF
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Received on Tue Feb 25 2014 - 10:00:07 PST
