Hello,
I assume that you mean pull_pbcatom0...
Nothing changes when I set this to an atom index I am afraid.
I saw that you had use pull_geometry=cylinder in your recent JACS paper.
Would it be too much to ask to see those pull settings?
I simply cannot get the molecule to stay at the desired
Hi,
we had similar trouble some time ago, and we could solve it by using a
good PBC atom. Make sure that your pbc_atom is in the very center of
your membrane.
Btw, using distance to compare with cylinder is a bad test, since it
does something very different (the distance is the same at
Is the problem specific to cylinder geometry? Do other settings work? Does
it
make a difference if you set values for pull_r0 and pull_r1?
-Justin
I would think that it is the cylinder geometry that creates the problem.
If I use
pull= umbrellapull_geometry
On 4/29/12 4:46 AM, J B wrote:
Is the problem specific to cylinder geometry? Do other settings work? Does it
make a difference if you set values for pull_r0 and pull_r1?
-Justin
I would think that it is the cylinder geometry that creates the problem.
If I use
pull = umbrella
Does the cylinder geometry work if you use pull_start = no and pull_init1
equal to your starting (restraint) distance? I'm just trying to go through
all
of the iterations of what might be failing. In theory, what you're doing is
fine but I'd be interested to know if there was something
On 4/28/12 5:12 AM, J B wrote:
Hi.
I am trying to the the PMF of transferring a drug molecule from the aqueous
phase to a lipid bilayer.
In order to minimize the effects of membrane undulations I tried to use
pull_geometry=cylinder.
Whenever I run a short simulation with umbrella sampling
Hi,
the distance is 3.89 nm and the z-dimension is roughly 8 nm
Date: Sat, 28 Apr 2012 09:18:31 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with
pull_geometry=cylinder
On 4/28/12 5:12 AM, J B wrote
-0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with
pull_geometry=cylinder
On 4/28/12 5:12 AM, J B wrote:
Hi.
I am trying to the the PMF of transferring a drug molecule from the aqueous
phase to a lipid
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