RE: AMBER: minimization

From: Ross Walker <>
Date: Fri, 31 Oct 2008 08:44:49 -0700

Hi Jacopo

> this is my input
> Minimization
> &cntrl
> imin=1, maxcyc=20000, NCYC=5000
> ntpr=500, scee=1.2, cut=10.0, drms=0.001,
> &end

I would start by just running 10 steps, set maxcyc and ncyc to 10 and then
set ntpr=1 so you get output on every step.

> 1500 -6.1989E+07 9.5130E+10 3.4646E+13 O 39074

This is step 1500. You need to see what it is on step 1. By step 1500 the
structure is probably already hopelessly distorted and 39074 is probably not
the atom that caused the original problem. Note though that your maximum
force is 3.5x10^13 which is huge so you definitely have a problem with your
initial structure.

> BOND = 621297.4559 ANGLE = 12297.8211 DIHED =
> 9920.4195
> VDWAALS = 1088705.3404 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = 4105.3057 1-4 EEL = 43532.3673 RESTRAINT =
> 0.0000

The *'s mean that the value is too large to fit in the space provided in the
output. Note the electrostatics are q1*q2/xR so as R goes to zero so the
electrostatic energy tends to infinity this is your problem here. Note also
that your VDWAALS and BOND energies are huge as well suggesting a very
strained bond but since this is for step 1500 of an already flawed
minimization it is impossible to tell the origin of this. I would go back,
look at step 1. See where the problems are, see what atom has the highest
force. Then load the prmtop and inpcrd file into something like VMD and have
it highlight that atom for you and then look to see if things make sense.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Nov 02 2008 - 05:08:19 PST
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