[gmx-users] Gas phase simulation

Wed May 6 16:23:05 CEST 2015

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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