Re: hole on the surface of the waterbox

From: Ana Vila Verde (
Date: Fri Aug 28 2009 - 06:19:41 CDT

yup! In NVT, there is no way your system can equilibrate to reach the
correct water density. I think all simulations using explicit solvent
must start with NPT equilibration for this reason (unless they're a
restart of a previous simulation which was already equilibrated.)

Fix the protein during equilibration, and slowly release it once you
think the water is OK. I think there's something in the NAMD manual or
in previous messages posted here that tells you how to go about
equilibrating systems.

Hope it helps,


Mert Gür wrote:
> Dear Ana,
> I performed my simulation for a T,V,N ensemble and I started to see
> this hole after 1 ns.
> Do your comments still hold?
> Best,
> Mert
> On Fri, Aug 28, 2009 at 1:54 PM, Ana Vila Verde <
> <>> wrote:
> Dear Mert,
> It's possible (actually, likely) that you started very far from
> the necessary water density. When this happens, the system cannot
> equilibrate volume rapidly enough (I'm assuming you're running in
> NPT) so you see thosewater holes. The solution: build your system
> from scratch adding more water molecules close to the protein and
> run in NPT for long enough until the volume equilibrates. If that
> doesn't work, then doing several cycles where you first run NVT at
> high temperature for about 0.5 ns (t=700 K, so the water
> "evaporates" and fills the hole) with the protein fixed followed
> by your normal NPT should speed up equilibration.
> I think the best way to check for this sort of problem is really
> looking at the DCD using VMD
> I hope it helps,
> Ana
> Mert Gür wrote:
> Dear all,
> I am performing MD simulation of crambin in a large waterbox
> (20 A cushion) with periodic boundary conditions. I don't use
> any rigid bonds.
> When I load my dcd file it seems that there is a hole on the
> surface where there are no watermolecules. But I came to this
> conclusion simply looking at the video. The protein stays in
> the middle of the waterbox during the simulations.
> Does that mean there is anything wrong with my simulation? Can
> this kinda behaviour happen for the water solvent? Is there a
> fast way to check if there really is a hole without looking
> at the video file (Maybe the video is just misleading me;
> there is no hole)?
> I attached my conf file in case you want to check it.
> Best,
> Mert

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