[gmx-users] Gas phase simulation

gozde ergin gozdeeergin at gmail.com
Fri May 8 17:47:44 CEST 2015 

Thanks a lot for your suggestions Chris.
I will try them and share the results with you.

Bests

On Thu, May 7, 2015 at 12:24 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> 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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