Re: [AMBER] Query- Heating after Equilibration

From: case <>
Date: Wed, 23 Jun 2010 00:43:19 -0400

On Wed, Jun 23, 2010, Jagdeesh C wrote:

> Thank you very much for your inputs Professor Case and Jason! I seem to have
> identified the problem. It had someting to do with the rst file. But, I
> don't know the solution to it.
> I performed 2 sets of minimization and then went on to perform the MD.
> 1) 1000 steps of steepest descent
> steepest
> &cntrl
> imin=1, ntmin=2, maxcyc=1000,
> cut=10.0,ntb=1,
> ntc=2,ntf=2,
> ntpr=100,
> /
> 2) This is followed by 1000 steps of Polak-Ribiere conjugte gradient
> polak
> &cntrl
> imin=1, ntmin=3,
> irest=0, ntx=1,
> maxcyc=1000,
> cut=10.0,ntb=0,
> ntc=2,ntf=2,
> ntpr=100,
> drms = 0.0119,
> /
> &lmod
> xmin_method = prcg,
> /
> Now when I perform subsequent MD simulations (input file shown below) with
> the rst generated from the first step they work fine. But, when I try them
> with the rst generated from the PRCG (second) step no output files are
> generated.

The second minimization step sets ntb=0, which will probably do really weird
things since you seem to have a periodic system. It's a little hard to see
what would cause "no output files" however. One of the first things sander
does is to write a header to the output file, along with a copy of the input.
Is there a chance that errors going to standard error (stderr) are being lost?
Are you sure you have a non-empty input coordinate file?

Anyway, you certainly have to fix the value of ntb, if you indeed want to do
the second minimization (it's not clear why this is desirable, however.)

> Here is the input for subsequent simulations using rst's generated from 1
> & 2
> MD
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=25000,dt=0.002,
> ntc=2,ntf=2,
> cut=10.0, ntb=2,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> ntp=1,taup=2.0,
> /*
> *

There are lots of problems with the above. First, you are asking for 25000
steps...when you are having problems, ask for 25 steps, set ntpr to 1, and
carefully study the output.

You should first equilibrate at constant volume (ntb=1) and only do constant
pressure (ntb=2) as a second step. It is dangerous to use dt=0.002 for
initial equilibration. There is probably no good reason to set the cutoff
to 10 -- keep it at its default value.


AMBER mailing list
Received on Tue Jun 22 2010 - 22:00:07 PDT
Custom Search