Re: hole on the surface of the waterbox

From: Mert Gür (
Date: Fri Aug 28 2009 - 07:20:09 CDT

Thanks Ana I totally got your point. Do you think that NPT equilibration
will significantly change my protein fluctuations in the N,V,T simulation?
If yes why?

On Fri, Aug 28, 2009 at 2:19 PM, Ana Vila Verde <>wrote:

> 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,
> Ana
> 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 <<mailto:
>>>> 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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