On 9/1/13 1:39 AM, Shima Arasteh wrote:
Hi,
I ran US on an ion through a channel inserted in a bilayer.
I used g_wham and got the profile output. In the visualized profile, I see a
region that the plot shows a flat line and it seems the data is missed there.
Would you please let me know wh
Hi,
I ran US on an ion through a channel inserted in a bilayer.
I used g_wham and got the profile output. In the visualized profile, I see a
region that the plot shows a flat line and it seems the data is missed there.
Would you please let me know what the reason of missing data is?
Thanks
Hello Gromacs users,
The solution that ended up working is selecting a different pull_pbcatom0
from the reference group, the protein, such that the atom is approx. in the
center of mass of the protein.
I hope that others may find this useful,
Thanks to Martin Vesper and Justin Lemkul for their i
Thank you all for your help,
Sheeba-
Yes, I get both positive and negative results. I think what you describe is
what I would get if I used 'distance' for the geometry.
In any case, I have values from +2 to about -3, and they are not evenly
distributed (unlike the coordinates, which are more or le
On 9/10/12 9:30 PM, Jianguo Li wrote:
I guess is that g_wham takes the distance from tpr file which calculates the
distance using grommp.
It seems that the distances calculated using g_dist and grompp are different,
as discussed in this forum about 10 days ago.
This is a fairly frequent c
: Discussion list for GROMACS users
Cc:
Sent: Monday, 10 September 2012, 23:54
Subject: Re: [gmx-users] umbrella sampling (PMF) position discrepancy
Hi Justin, thank you for you quick reply.
On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote:
>
>
> On 9/10/12 11:22 AM, Raphael Alhad
Hi Justin, thank you for you quick reply.
On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote:
>
>
> On 9/10/12 11:22 AM, Raphael Alhadeff wrote:
>
>> Dear Gromacs users,
>>
>> I've been trying to run an umbrella sampling (for the purpose of pmf)
>> using
>> Gromacs 4.5.5.
>> My system consists
On 9/10/12 11:22 AM, Raphael Alhadeff wrote:
Dear Gromacs users,
I've been trying to run an umbrella sampling (for the purpose of pmf) using
Gromacs 4.5.5.
My system consists of a membrane protein transporter and a Na ion passing
through it, from the water bulk on one side of the membrane to t
Dear Gromacs users,
I've been trying to run an umbrella sampling (for the purpose of pmf) using
Gromacs 4.5.5.
My system consists of a membrane protein transporter and a Na ion passing
through it, from the water bulk on one side of the membrane to the water
bulk on the other side. I've used the pr
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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