Re: hole on the surface of the waterbox

From: Mert Gür (gurmert_at_gmail.com)
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?
Best,
Mert

On Fri, Aug 28, 2009 at 2:19 PM, Ana Vila Verde <a.vilaverde_at_amolf.nl>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 <a.vilaverde_at_amolf.nl<mailto:
>> a.vilaverde_at_amolf.nl>> 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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