On 5/13/13 5:33 AM, Arunima Shilpi wrote:
Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error
Here I have new set of queries..
How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-a
Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error
Here I have new set of queries..
How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-axis/...
and which all conf file should i take
On 5/7/13 1:05 AM, Arunima Shilpi wrote:
Hello Justin sir
In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as
editconf -f complex.gro -o newbox.gro -center 3.280 2.181
Hello Justin sir
In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as
editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12
--
Thanking Y
On 12/10/12 5:18 AM, Anders Lervik wrote:
Dear all,
I have been simulating an inhomogeneous system consisting of a membrane and
a solvent (e.g a lipid bilayer solvated in water). In these simulations, I
have noticed lateral movement in the COMs of the membrane and solvent -
they move in opposi
Dear all,
I have been simulating an inhomogeneous system consisting of a membrane and
a solvent (e.g a lipid bilayer solvated in water). In these simulations, I
have noticed lateral movement in the COMs of the membrane and solvent -
they move in opposite directions such that the overall center of
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and
membrane,which looks like this:
pull = umbrella
pull_geometry= cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim =
Dear GMX users,
I am using pull code to make a distance restrain to my proteins and
membrane,which looks like this:
pull = umbrella
pull_geometry= cylinder
pull_vec1 = 0 0 1
pull_r1 = 2.5
pull_r0 = 2.5
pull_dim =
gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Monday, September 26, 2011 1:32 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Center of mass: distance restrain for groups
>
> Justin A
it this keyword.
-Justin
Best,
Hualin
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 1:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of ma
[gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 1:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Justin A. Lemkul wrote:
>
>
> Li, Hualin wrote:
>> I a
Justin A. Lemkul wrote:
Li, Hualin wrote:
I am sorry about the last post, I mean "I am not sure about the word
"pullumbrella", is this command used in free energy
calculation to do the sampling ? I am not doing the free energy
calculation, should I change something in the
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 12:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Li, Hualin wrote:
Dear G
Thanks,
Hualin
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 12:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distan
ase?
Thanks,
Hualin
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, September 26, 2011 12:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Li, Hual
Li, Hualin wrote:
Dear GMX users,
How are you doing? I have a question about using distance restrain in
GROMACS, have you ever use the distance restrain to between the protein and the
center of mass of membrane. In gromacs, I can not find the option to choose the
center of mass of speci
Dear GMX users,
How are you doing? I have a question about using distance restrain in
GROMACS, have you ever use the distance restrain to between the protein and the
center of mass of membrane. In gromacs, I can not find the option to choose the
center of mass of specific groups like membra
On 28/01/2011 4:25 AM, WU Yanbin wrote:
Dear GMXers,
I would like to reproduce the water droplet contact angle on graphite
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.;
Koumoutsakos, P. /J. Phys. Chem. B/ *2003*, /107/, 1345-1352.
The box size is 20nm by 20nm by 30nm. Graphite i
Dear GMXers,
I would like to reproduce the water droplet contact angle on graphite
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P.
*J. Phys. Chem. B* *2003*, *107*, 1345-1352.
The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer
carbon sheet. Af
One trick I am working with right now, is to have
- periodic boundary conditions only xy
- remove the COM motion of the water and the graphite separately. The COM
motion is now removed only in the xy direction, so they are free to move in z.
- put the surface (your graphite) at coordinate 0
- enab
Dear gmx-users,
It is known that if system have an absolute reference, the removal of
COM could lead to artifacts. However, for instance, when one water
slab adsorbs on a freezed, infinite graphite surface, the COM motion
is still free in x or y direction, and subsequently leads to net flows
durin
Thank you
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] center of mass
Date: Mon, 16 Mar 2009 17:56:16 +0100
On Mar 16, 2009, at 5:51 PM, Antonia V. wrote:Hello,
I am wondering if there is a tool implemented in GROMACS that computes the
coordinates of the center
On Mar 16, 2009, at 5:51 PM, Antonia V. wrote:
Hello,
I am wondering if there is a tool implemented in GROMACS that
computes the
coordinates of the center of mass of each molecule of a simulation
box.
g_traj -f traj.xtc -com
Thank you
Antonia
Invite your mail contacts to join your fri
Hello,
I am wondering if there is a tool implemented in GROMACS that computes the
coordinates of the center of mass of each molecule of a simulation box.
Thank you
Antonia
_
Invite your mail contacts to join your friends list with
Tsjerk Wassenaar wrote:
Hi [EMAIL PROTECTED],
I have recently modified the routine as to not crash upon a shift over
periodic boundaries, which would occur with the original code. Also, I
streamlined the routines such that they don't lead to large
modifications of update.c
I will put the modifie
Hi [EMAIL PROTECTED],
I have recently modified the routine as to not crash upon a shift over
periodic boundaries, which would occur with the original code. Also, I
streamlined the routines such that they don't lead to large
modifications of update.c
I will put the modified code on line, probably t
Hi all,
searching in the ml I found this thread:
http://www.gromacs.org/pipermail/gmx-users/2006-April/021256.html
about comm-mode=angular and the method described in
J. Chem. Phys. 112(1) pp. 9-23 to remove com translation and rotation.
I was not able to download the modified versions of the co
On Thu, 27 Dec 2007 08:55:03 +0100
"Tsjerk Wassenaar" <[EMAIL PROTECTED]> wrote:
Hi,
Just to add my 5 cEUR. The flying ice cube will be avoided using linear comm
removal on the whole system (default), which will retain diffusion of the
peptide in the solvent.
Thanks Tsjerk for clarifying my
Hi,
Just to add my 5 cEUR. The flying ice cube will be avoided using linear comm
removal on the whole system (default), which will retain diffusion of the
peptide in the solvent. The peaks you see in the comm I guess are due to the
update of the neighbour list (every ten steps?). This will change
On Wed, 26 Dec 2007 09:01:22 +0100
David van der Spoel <[EMAIL PROTECTED]> wrote:
Li Qiang wrote:
hi Christian,
Thanks for the reply. I have plotted the the rate of center of mass
motion and found there are peaks with certain time interval. I think
that is not only a visual problem but like fl
Li Qiang wrote:
hi Christian,
Thanks for the reply. I have plotted the the rate of center of mass
motion and found there are peaks with certain time interval. I think
that is not only a visual problem but like fly ice cube problem(not
sure). As a comparison, when a large protein is simulated, th
Hi again,
this is the COM velocity of the peptide only? Then these peaks are
perhaps a PBC artifact?!
Actually I never saw such a fast movement in my runs so far that the
solute was speeding through the box over and over. But perhaps the
velocity is so high in your case that one has to take care
hi Christian,
Thanks for the reply. I have plotted the the rate of center of mass
motion and found there are peaks with certain time interval. I think
that is not only a visual problem but like fly ice cube problem(not
sure). As a comparison, when a large protein is simulated, the
rate(velocity) o
Li Qiang schrieb:
> Dear all,
Hi Qiang,
> I am simulating short peptide in GROMACS. Center of mass need to be
> removed to keep the peptide from jumping out.
I guess this is only a visual problem, but read page 18 in the manual.
> I have two questions about this:
> 1, when I remove COM of the p
Dear all,
I am simulating short peptide in GROMACS. Center of mass need to be
removed to keep the peptide from jumping out.
I have two questions about this:
1, when I remove COM of the peptide using comm_grps, do I need to put
the solvent(including the counter ion) at the same time for COM remov
> Dear all
> i want to determine the center of mass of my protein
> in the z-dimension.which command in gromacs is useful
> for me?
Did you look in section 7.3.12 of the manual? Demonstrating a credible
attempt to solve your own problem is much more likely to generate useful
answers for you. Peopl
mahbubeh zarrabi wrote:
Dear all
i want to determine the center of mass of my protein
in the z-dimension.which command in gromacs is useful
for me?
thanks
g_traj
Choose the right car based on your ne
Dear all
i want to determine the center of mass of my protein
in the z-dimension.which command in gromacs is useful
for me?
thanks
Choose the right car based on your needs. Check out Yahoo! Autos new Car
Cherry Y. Yates wrote:
Dear Gromacs users and developers,
I am studying a system consisting of six molecules (3 groups). I would like to
keep the center-of-mass motion of each molecule with the system having zero
center-of-mass motion. So I set comm_mode=Linear. In the simulation,
immediately th
Dear Gromacs users and developers,
I am studying a system consisting of six molecules (3 groups). I would like to
keep the center-of-mass motion of each molecule with the system having zero
center-of-mass motion. So I set comm_mode=Linear. In the simulation,
immediately the center-of-mass motion o
Jian Dai wrote:
Hello, everyone:
I have a system which is composed of a lipid bilayer and water layers
upon each monolayers.
Now the problem is that after the simulation, the lipid bilayer shift
upward inside the simulation box , and makes the upper water layer
thinner, while the lower water
Hello, everyone:
I have a system which is composed of a lipid bilayer and water layers upon
each monolayers.
Now the problem is that after the simulation, the lipid bilayer shift upward
inside the simulation box , and makes the upper water layer thinner, while
the lower water layer thicker.
In md
, Berk Hess wrote:
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] center of mass pulling in AFM
Date: Tue, 18 Jul 2006 14:41:53 +0200
Ok, that's what we thought. So would you think
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] center of mass pulling in AFM
Date: Tue, 18 Jul 2006 14:41:53 +0200
Ok, that's what we thought. So would you think that it is a b
Would you agree with that?
Thanks,
Kay.
On Jul 18, 2006, at 2:16 PM, Berk Hess wrote:
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] center of mass pulling in AFM
Date: Tue, 18 Jul 200
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] center of mass pulling in AFM
Date: Tue, 18 Jul 2006 12:44:20 +0200
We have a complex with two chains. From one chain (chain A),
, but artificially ) elongated due to the COM
fixing. Did I understand that correctly?
Thanks,
Kay.
On Jul 18, 2006, at 11:31 AM, Berk Hess wrote:
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: [gmx-
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: [gmx-users] center of mass pulling in AFM
Date: Mon, 17 Jul 2006 12:58:02 +0200
Hi there,
we are doing pulling simulations of protein complexes. For
Hi there,
we are doing pulling simulations of protein complexes. For these
simulations, we keep the COM of one group fixed and pull on the COM
of the other group. Now we got into this discussion, whether this
introduces artificial distortions on the hold protein. If the protein
deforms in
Thanks for the suggestion Xavier. However, I already tried g_mindist and the
problem is that it does not use the center of mass of the reference group to
calculate the distance to the atoms of the solvent group. Instead, it computes
all possible distances between pairs of atoms between the groups
On Thu, 4 May 2006 23:48:28 -0400 (EDT)
"YOLANDA SMALL" <[EMAIL PROTECTED]> wrote:
Hello,
I would like to determine the percentage of water
occupation in a protein region
by calculating the distance between the center of mass
of a group of atoms and
the solvent. Does anyone know which gromac
YOLANDA SMALL wrote:
Hello,
I would like to determine the percentage of water occupation in a protein region
by calculating the distance between the center of mass of a group of atoms and
the solvent. Does anyone know which gromacs tools can provide an estimate of
this information? By the way
Hello,
I would like to determine the percentage of water occupation in a protein region
by calculating the distance between the center of mass of a group of atoms and
the solvent. Does anyone know which gromacs tools can provide an estimate of
this information? By the way my trajectory is in xtc
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