users/2015-April/096847.html
> >
> > but you don;t say what they are (or I missed it).
> >
> > Chris.
> >
> > ________________
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.
0:23
To: gmx-us...@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 pul
th.se> on behalf of gozde
> ergin
> Sent: 06 May 2015 04:28
> To: gmx-us...@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
...@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
f gozde
> ergin
> Sent: 05 May 2015 08:57
> To: gmx-us...@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
>
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gozde ergin
Sent: 05 May 2015 08:57
To: gmx-us...@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
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
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 t
Dear Gromacs users,
In order to estimate the free energy profile of water on organic
coated-water system I am using Gromacs umbrella option.
I put my water molecule far away from the bulk organic+water system and
pulled this molecule through the bulk.
When I checked the PMF profile I realized that
