Re: hole on the surface of the waterbox

From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Aug 28 2009 - 13:45:03 CDT

Ana,
Thanks for your insightful explanations .
Best,
 Mert

On Fri, Aug 28, 2009 at 3:48 PM, Ana Vila Verde <a.vilaverde_at_amolf.nl>wrote:

> As to the choice between NVT and NPT production runs: in principle they
> should produce the same thing; in practice, NVT production runs are often
> preferred because, like you said, they keep the simulation procedure simple.
> So, I would go for NPT equilibration and NVT production runs whenever
> possible.
> Cheers!
>
> Ana
>
>
>
> Mert Gür wrote:
>
>> Dear Ana,
>> Thanks for your quick response. I am aware of this procedure. Actually the
>> way I performed the T,V,N ensemble was the reason to keep my simulation as
>> simpleand fast as possible.
>> My question was actually how much dou you think my protein fluctuations
>> will change by performing the procedure you just stated, compared to the
>> ones I already have.
>> My expectation is that they won't change significantly.
>> I will perform the simulation also as you suggest anyway. But it would be
>> nice also have your opinion on that.
>> Best,
>> Mert
>>
>> On Fri, Aug 28, 2009 at 3:26 PM, Ana Vila Verde <a.vilaverde_at_amolf.nl<mailto:
>> a.vilaverde_at_amolf.nl>> wrote:
>>
>> Equilibration is a somewhat violent process during which water
>> density and structure change very rapidly. This may significantly
>> disturb the structure of your protein in ways that are not
>> physical. If the disturbance is great, the protein may be stuck
>> in a local energy minimum and may not be able to get back to the
>> minimum energy structure during the duration of your simulation.
>> If we agree that the experimental structure is the gold standard,
>> you want to keep the starting protein structure for your
>> production runs as close as possible to the experimentally
>> observed one. hence, always fix the protein during equilibration;
>> release it slowly only at the end of equilibration, and then run
>> your production simulations.
>>
>> Cheers,
>>
>> Ana
>>
>>
>> Mert Gür wrote:
>>
>> 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 <mailto:a.vilaverde_at_amolf.nl>
>> <mailto:a.vilaverde_at_amolf.nl <mailto: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>
>> <mailto:a.vilaverde_at_amolf.nl <mailto:a.vilaverde_at_amolf.nl>>
>> <mailto:a.vilaverde_at_amolf.nl
>> <mailto:a.vilaverde_at_amolf.nl> <mailto: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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