[gmx-users] Gas phase simulation

Thu May 7 00:58:16 CEST 2015

As a debugging method, I'd suggest to try pulling out the other side, from water directly into vacuum. I have no idea what the dG should be from organic solvent to vacuum but the value for water to vacuum is quite well established, both from expt. and simulation with many different force fields.

I'll not that you've got *way* more umbrellas than you need (though that should not be a problem, just an inefficiency).

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gozde ergin <gozdeeergin at gmail.com>
Sent: 06 May 2015 10:23
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Gas phase simulation

I am pulling one water molecule from gas phase center of mass of bulk water
which z position is 6 nm.
However in PMF figure 0 means the limit position which 6 nm in real. PMF
shows the distance between the center of mass and pulled molecule.
I put my water molecule (which is A in .mdp file)  5 nm far away from the
center of mass of water bulk. That means the pulled molecule correct z
position in 6+5 = 11 nm.
As you can see from density figures, bulk water position is between 4-7.5
nm, and organic layer position is 7-9.5 nm. Which means by pulling from
11nm to 6 nm I am passing from organic layer and reached the water bulk.

In mdp file:
A is one water molecule
B is the bulk water

Maybe I should play with pulling rate and force constant?

On Wed, May 6, 2015 at 2:34 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> Why do images 4 and 5 show a length of 20 nm but your PMF and histograms
> only go 5 nm? Based on Figs 4 and 5, 5 nm is insufficient to go from bulk
> water through the organic solvent to vacuum.
>
> Also, what are your groups for pulling? I see you define groups A and B in
> your .mdp from:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096847.html
>
> but you don;t say what they are (or I missed it).
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gozde
> ergin <gozdeeergin at gmail.com>
> Sent: 06 May 2015 04:28
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Gas phase simulation
>
> Dear Neale,
>
> Here is the link for the images.
>
>
> http://imgur.com/KbmB3az,59vNExc,LfPFuP4,SGapfFv,uLt2roA,kmn6KCH,wSqaDlH,l207jLG#0
>
> I put density profile when solute in gas and organic phase. I also put
> their snapshots from VMD.
> There are two more figures to check the statistics which are bsProfs and
> bsResult.
> There is also histogram image.
>
> On Tue, May 5, 2015 at 5:40 PM, Christopher Neale <
> chris.neale at alum.utoronto.ca> wrote:
>
> > post the images elsewhere and the post a link on this list. I did not get
> > the attachment.
> >
> > Can you also post an image of one umbrella where the solute is in the
> > organic phase and one image of an umbrella where the solute is in the gas
> > phase?
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gozde
> > ergin <gozdeeergin at gmail.com>
> > Sent: 05 May 2015 08:57
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Gas phase simulation
> >
> > Actually during the simulation none of my organic molecules evaporate.
> > I restraint the heavy atom of organic molecules in order to capture the a
> > maxima (increment) on free energy from gas phase to organic phase.
> >
> > For the same system I also applied impinging method which I put 100 water
> > molecules on gas phase above the organic + water system. Only 20 of them
> > were absorbed&adsorbed by organic+water phase and 80 of them scattered
> from
> > organic surface. I wanted to strength these result by doing umbrella
> > sampling.
> >
> > As a theory if a water molecules could not enter the organic coated water
> > bulk phase, there should be barrier on free energy from gas phase to
> > organic layer which prevent this gas phase molecule to be absorbed by
> bulk
> > phase. However I can not capture this maxima on free energy if I do not
> > restraint my organic molecules.
> >
> > Here you can find my density profile for water and organic layer.
> >
> > 
> >
> > On Tue, May 5, 2015 at 2:32 PM, Christopher Neale <
> > chris.neale at alum.utoronto.ca> wrote:
> >
> > > Dear Gozde:
> > >
> > >
> > > There are a few questions:
> > >
> > >
> > > 1. Does your system remain triphasic? You can check quickly one system
> > > with VMD or you can do it quantitatively with g_density (separate
> > profiles
> > > for all-atoms, water, organic solvent). I see a triphasic system in
> your
> > > image but that doesn't guarantee that it stays this way.
> > >
> > >
> > > 2. I'm presuming that you added the restraints on the organic molecules
> > > because they were boiling away. Why is this? I don't know. Is your
> > organic
> > > solvent expected to be volatile at your simulation temperature? Maybe
> the
> > > ff is wrong or maybe this is what should be happening.
> > >
> > >
> > > 3. I can't address how to correct for the presence of restraints unless
> > > you tell us how did you add these restraints? If you're doing absolute
> > > position restraints then I'd say you're doing it wrong. Here's what I
> > would
> > > do.
> > >
> > >
> > > a) simulate a biphasic water/organic solvent system (no vacuum) at NPT.
> > >
> > > b) find the average box volume from that simulation
> > >
> > > c) select a frame that is closes to this average volume
> > >
> > > d) extend your box along z to create a vacuum region
> > >
> > > e) add an enormous number of flat-bottom position restraints (one for
> > each
> > > molecule) along z to keep the water in the water region and the
> organics
> > in
> > > the organic region but to not apply any force while they are in that
> > region.
> > >
> > > f) do your umbrella sampling on this system using NVT
> > >
> > >
> > > *** You're not going to get the interfaces correct with this design.
> > > Therefore, your profiles will be wrong but the overall dG of transfer
> > > should still be correct. You could probably use only a single
> flat-bottom
> > > half-harmonic on each organic solvent molecule to stop it from
> > evaporating
> > > and let the water/air and water/organic interfaces sort themselves out.
> > > That way, you only really perturb the organic/air interface (and then
> > there
> > > is also no need for the initial NPT to evaluate average volume and also
> > you
> > > can do the US in NPT).
> > >
> > >
> > > Nevertheless, the above is just one hack to force your system to behave
> > as
> > > you are asking it to. It's probably better to figure out i) if it is
> > > behaving physically realistically and ii) if not then why not (i.e.,
> > adjust
> > > the parameters).
> > >
> > >
> > > Chris.
> > >
> > >
> > > ________________________________
> > > From: gozde ergin <gozdeeergin at gmail.com>
> > > Sent: 05 May 2015 07:16
> > > To: Christopher Neale
> > > Subject: Fwd: About 2011 paper
> > >
> > >
> > > ---------- Forwarded message ----------
> > > From: gozde ergin <gozdeeergin at gmail.com<mailto:gozdeeergin at gmail.com
> >>
> > > Date: Tue, May 5, 2015 at 12:13 PM
> > > Subject: About 2011 paper
> > > To: nealec at rpi.edu<mailto:nealec at rpi.edu>
> > >
> > >
> > > Dear Dr. Neale,
> > >
> > > After I read your 2011 paper about the umbrella sampling I would like
> to
> > > ask you some questions.
> > >
> > > I am also running umbrella sampling simulation by Gromacs.
> > > My system has 860 water molecules covered by 50 organic molecules.
> > > My purpose is to estimate the PMF profile of a water molecule from bulk
> > > water to gas phase (reaction coordinate in order : bulk water->organic
> > > layer->gas phase) Please check 1_system.png.
> > >
> > > In order to do that I picked a water molecule from bulk water and
> pulled
> > > it through the reaction coordinate. I would like see change in PMF from
> > > bulk to organic and organic to gas phase. However I could not see any
> > > difference between organic to gas phase. Please check
> > > 2_without_restraint.jpg
> > >
> > > Thereafter I thought I maybe should restraint my organic molecules
> > > position to reduce their effect on gas phase free energy.
> > > By doing so I managed to see the change in PMF from organic layer to
> gas
> > > phase. Please check 3_with_restraint.jpg
> > >
> > > But by restraining organic molecules positions I added an extra force
> on
> > > system.
> > > Now I could not figure out what should I do to minimize the effect of
> > > positions restraint?
> > > Also another question why I could not sample the gas phase without
> > > restraining my organic molecules?
> > >
> > >
> > > In figures, z=0 the middle of the water bulk
> > >                z>4 gas phase
> > >                2<z<4 organic phase
> > >
> > >
> > > Any suggestions will be appreciated. Thanks in advance.
> > >
> > > --
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