Re: Re :AMBER: Holes in water

From: Lukasz Bielecki <>
Date: Sat, 12 Mar 2005 17:52:31 +0100 (CET)

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,


On Fri, 11 Mar 2005, Pascal Auffinger wrote:

> Well its quite easy. During the setting up of the system there is just
> 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
> 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
>> 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 - 17:53:00 PST
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