Re: hole on the surface of the waterbox

From: Mert Gür (
Date: Fri Aug 28 2009 - 06:12:25 CDT

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?

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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