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 z-po
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 z
> 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 som
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
pull
> 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
: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:
> > Hi.
> >
> > I am trying to the the PMF of tra
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:
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 st
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 starting from a
configuration with
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