[gmx-users] Gas phase simulation
gozdeeergin at gmail.com
Wed May 6 10:28:11 CEST 2015
Here is the link for the images.
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
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
> 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
> 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
> > 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
> > 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
> > 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
> > molecule) along z to keep the water in the water region and the organics
> > the organic region but to not apply any force while they are in that
> > 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
> > and let the water/air and water/organic interfaces sort themselves out.
> > That way, you only really perturb the organic/air interface (and then
> > is also no need for the initial NPT to evaluate average volume and also
> > can do the US in NPT).
> > Nevertheless, the above is just one hack to force your system to behave
> > 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.,
> > 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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