Re: hole on the surface of the waterbox

From: Ana Vila Verde (a.vilaverde_at_amolf.nl)
Date: Fri Aug 28 2009 - 07:48:35 CDT

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
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:21 CST