On 8/19/13 12:27 PM, Za Pour wrote:
Dear gmx-users
Iwould like to calculate the PMF between two nanotubes covered
with some molecules. To do that, one nanotube has to be held fixedly and
another one
is supposed to be moved as a rigid entity. To generate configurations, for
fixed nanotube
Dear gmx-users
Iwould like to calculate the PMF between two nanotubes covered
with some molecules. To do that, one nanotube has to be held fixedly and
another one
is supposed to be moved as a rigid entity. To generate configurations, for
fixed nanotube
I used
position restraints in all direc
Sir
I have query as to how to go ahead for potential mean force (PMF)
calculation between protein and ligand. As per the umbrella sampling
protocol you have provided us in gromacs tutotrial it says it is for
protein molecules...
--
Thanking You with Regards.
Arunima Shilpi
Ph. D Research Scho
=
Message: 4
Date: Wed, 02 Dec 2009 08:42:36 -0500
From: chris.ne...@utoronto.ca
Subject: [gmx-users] PMF calculation using g_wham using different
simulationboxes
To: gmx-users@gromacs.org
Message-ID: <20091202084236.bk7yqoke0w0wc...@webmail.utoronto.ca>
Content-T
Hi Li,
In my opiniun, what you propose is acceptable, but not rigorous, and
you will need to prove that there are no unexpected artifacts of
changing box size. For example, you should definitely run a couple of
your small box systems as larger boxes as well and show that you get
the same
Li Jianguo wrote:
Hi
I am trying to calcualte the potential of mean force between two
polyatomic particles using umbrella potential and the g_wham command. I
need to run multiple windows from close to far inter-particle distance.
To save time, I used smaller box sizes for those windows wit
Hi
I am trying to calcualte the potential of mean force between two polyatomic
particles using umbrella potential and the g_wham command. I need to run
multiple windows from close to far inter-particle distance. To save time, I
used smaller box sizes for those windows with shorter inter-parti
1: Did you "constrain" or "restrain" the distance? Providing your .mdp
file would help us to figure this out. The terms are quite different
on this list.
2: The atom "danced around the expected position" ... are you sure
that it "danced" around x and z, not just Y?
3: If your distance is
Dear gmx-users:
I am performing a PMF calculation using the pull code. I selected one fixed
atom as a reference group and constrained another atom with respect to this
reference group so that their separation in the x- and z-directions remain
constant. After running the simulation, I visualized th
Dear Mr Mark Abraham:
Can you tell us the details of performing PMF procedures? Thank you very
much!
Best wish for you!
Mark Abraham <[EMAIL PROTECTED]> 写道：
> Dear all,
> I am working on a tripeptide and would like to calculate Potential
> Mean Force for the tripeptide. Suggestions to cal
> Dear all,
> I am working on a tripeptide and would like to calculate Potential
> Mean Force for the tripeptide. Suggestions to calculate PMF are
> awaited.
How about looking for PMF in the manual and reading what it has to say there?
Mark
___
gmx-use
Dear all,
I am working on a tripeptide and would like to calculate Potential
Mean Force for the tripeptide. Suggestions to calculate PMF are
awaited.
Regards,
Chetana
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