It is likely an electrostatic collapse (electrostatic stronger than vdw so atoms of opposite charge overlap and cannot be overcome by minimization) OR bad parameters.
I minimize first, turning off electrostatics, to get the vdw resolved and this usually works. If it doesn't, bad parameters somewhere...
min_noelec.in:
relax vdw
&cntrl
imin = 1, maxcyc = 300, ncyc = 300,
ntb = 2, ntp = 1,
cut = 9.0,
iwrap = 1,
lastist = 10000000,
lastrst = 10000000,
nmropt = 1,
&end
&wt
type = 'ELEC', value1 = 0.0,
&end
&wt
type = 'END',
&end
DISANG=inputs/restraints.in
LISTOUT=POUT
Create a separate file called restraints.in
&rst iat = 0, &end
--tec3
________________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Tuesday, January 5, 2021 9:01:06 PM
To: amber.ambermd.org
Subject: Re: [AMBER] NaN VDWAALS Error During Minimization
That's a suggestion for devs to discuss among themselves, in case any
missed it. :-)
Bill
On 1/5/21 7:45 PM, Bill Ross wrote:
> The atom with max gradient is printed at each step. Maybe having the top
> two atoms would help, or any atom with a big diff from the rest should
> also be printed?
--
Phobrain.com
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Received on Tue Jan 05 2021 - 21:00:02 PST
