Re: AMBER: heating

From: Ilyas Yildirim <>
Date: Tue, 8 Mar 2005 18:02:17 -0500 (EST)

Hi Gustavo,

I had vlimit problem too, but my case was a little bit different. I used

SolvateOct methane TIP3PBOX 8.0

to solvate the solute. And when I tried to heat the system (or
equilibrate), I had this vlimit problem. It seems that I had to solvate
the system with a 12.0 A thickness to get rid of vlimit problem. Maybe
that is the reason in your case too; you should increase the thickness of
the solvent shell.

Good luck,

PS: How is your sander input file?

On Tue, 8 Mar 2005, Gustavo Pierdominici Sottile wrote:

> Dear Amber users,
> I have the problem of the vlimit exceded as soon as
> I start the heating. What I did is this: from the crystallografic pdb , I
> use leap with the option solvateCap so as to have the protein in a sphere.
> The I practiced a quit optimization , and with the last structure I used it
> to start the heating procedure. Using both tempi=0.0 (so velocities are
> calculated from the forces), or tempi=1.0 (so as to try other thing) ; the
> problem of vlimit exceded appears at the step number 80. Then it goes on and
> explotes.
> I see the initial structure and seems to be write. When I use solvateCap of
> tleap the parameter [closeness] is the default one (1.0)
> I use amber7
> If someone knnows what is happening and/or how can I do to see which is the
> reason of the problem, please write me
> Thanking in advance
> Gustavo

  Ilyas Yildirim
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
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Received on Tue Mar 08 2005 - 23:53:00 PST
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