Re: [AMBER] NaN VDWAALS Error During Minimization

From: Thomas Cheatham <tec3.utah.edu>
Date: Wed, 6 Jan 2021 04:33:17 +0000

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
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