Re: Re :AMBER: Holes in water

From: Carlos Simmerling <>
Date: Sat, 12 Mar 2005 13:32:06 -0500

is it possible that you are restraining the water back to the initial
positions? that would re-form the holes. try using the restraints
during the pressure equilibration too.
please let us know what your coordinates for -ref are and
what your restraintmask is. also the first energy evaluation
with the restraint energy. check the sander output when it
processes the restraintmask - is it correct?

don't mix the terms constraint and restraint, they mean
very different things. you are using restraints, not constraints.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Lukasz Bielecki wrote:

> Thanks for the hints but actually I AM using the constant pressure MD
> and this is where the holes/voids do form. In fact, after the belly
> stage of the NPT dynamics, the system is well equilibrated, with the
> volume shrinked exactly as in the manual - and then at the next stage
> - where I am using positional constraints (NTR=1; RESTRAINT_WT and
> RESTRAINTMASK parameters used - it is AMBER 8), the system again
> expands and holes form. It is constant pressure, as well here.
> Interestingly, when I am deleting the constraints from the input file
> (and set NTR to 0), the system does not expand and holes don't seem to
> emerge. So maybe there is some problem with the NTR=1 option? But I
> actually need constraints in my experiment, the unconstrained run was
> just a test.
> Thank you for your help,
> Lukasz
> On Fri, 11 Mar 2005, Pascal Auffinger wrote:
>> Well its quite easy. During the setting up of the system there is just
> no
>> way to get an optimal compaction of the solvent. Then during the MD the
>> system compacts itself, especially around the solute and then you get
> see
>> the formation of holes since the box size (pressure) cannot adjust.
>> Pascal
>>> Dear Amber experts,
>>> When I perform constant pressure MD of a nucleic acid in a TIP3P
> solvation
>>> box (PME), I get increasing holes or voids in the solvent part of the
>>> system. What can be the reason for this? The system seems to be well
>>> energy minimized, then smoothly heated to 300K, and at those initial
>>> stages no holes appear, only during the later production run.
>>> Many thanks for your help,
>>> Dr. Lukasz Bielecki
> On Fri, 11 Mar 2005, Bill Ross wrote:
>> See the FAQ on equilibration - constant pressure is needed to
>> let the box shrink to the correct density.
>> Bill
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> Lukasz Bielecki
> 'Health is merely the slowest possible rate at which one can die'
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Received on Sat Mar 12 2005 - 18:53:00 PST
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