Thank you Mark for reply.
as you said ...
Depends whether rigidity or scaling make more sense in your model of
real physics, which depends what's in your system.
My system is generally consist of proteins or peptides ( single ,
double or many)..
I am using option com Is it right
As per
On 15/08/2012 4:52 PM, rama david wrote:
Thank you Mark for reply.
as you said ...
Depends whether rigidity or scaling make more sense in your model of
real physics, which depends what's in your system.
My system is generally consist of proteins or peptides ( single ,
double or many)..
I am
Dear All,
I just installed a VMD. And then I load a gro file and a xtc file from a
simulation. The bar in the VMD Main window continuously moves, however the
protein molecule in the OpenGL Display window does not move.
Will you please tell me what is the problem, or how can see the whole
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6
13.6 13.6 -center 6.8 6.8 6.8
3-
Thanks a lot Mark!
Date: Wed, 15 Aug 2012 11:48:00 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Parameters for bonded interactions
On 15/08/2012 9:46 AM, Sebastien Cote wrote:
Dear Gromacs users,
In
After checking the post-processed topology, it does not contain the information
that I need. I would like to know the torsion angle parameters of each torsion
angle, and then compare with the ffbonded file to see the corresponding
four-atom groups ' X X X X '.
Is there a way to convert the
On 15/08/2012 8:44 PM, Sebastien Cote wrote:
After checking the post-processed topology, it does not contain the information
that I need. I would like to know the torsion angle parameters of each torsion
angle, and then compare with the ffbonded file to see the corresponding
four-atom groups
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6
13.6 13.6 -center 6.8 6.8 6.8
3-
Thanks Mark! This is exactly what I need.
Date: Wed, 15 Aug 2012 22:18:10 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Parameters for bonded interactions
On 15/08/2012 8:44 PM, Sebastien Cote wrote:
After
On 15/08/2012 10:27 PM, mohammad agha wrote:
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic
Hi,
I noticed that in my topology file, there is no inclusion of position
restraint file for my protein. For instance, my topology file looks
like this:
; Include forcefield parameters
#include gromos53a6.ff/forcefield.itp
; Include chain topologies
#include topol_Protein_chain_D.itp
#include
Is this because the topol_Protein_Chain_D.itp has a line of including
the position restraint file for chain D?
On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani
ankitanaith...@gmail.com wrote:
Hi,
I noticed that in my topology file, there is no inclusion of position
restraint file for my
Dear Mark,
Thank you very much from your help.
Best Regards
Sara
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday, August 15, 2012 5:23 PM
Subject: Re: [gmx-users] box of simulation
On
On 8/15/12 9:12 AM, Ankita naithani wrote:
Is this because the topol_Protein_Chain_D.itp has a line of including
the position restraint file for chain D?
Yes, #include statements for position restraint files are contained in each
chain topology.
-Justin
On Wed, Aug 15, 2012 at 2:05
Dear Gromacs users!
I want to obtain Cross-correlation maps ( for indication of the
cross-correlated fluctuations of the residues).
The example of such maps can be found here
http://pubs.acs.org/doi/abs/10.1021/ja076046a
I found that modificied version of the G_covar from users
contributions
hello:
Does anybody have any idea for the new version? when would it be
reachable? and what's new?
thx
Albert
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On Wed, Aug 15, 2012 at 4:31 PM, Albert mailmd2...@gmail.com wrote:
hello:
Does anybody have any idea for the new version? when would it be
reachable? and what's new?
You can always try the current version of any of the branches using
Git:
hello:
that's for kind reply.
The unreleased version probably is not stable enough. I am asking for
the official released version. As we can see the 4.5.5 is the one which
was released almost one year ago. Do you have any idea when the next
version would be officially released? And what's
On 8/15/12 11:09 AM, Albert wrote:
hello:
that's for kind reply.
The unreleased version probably is not stable enough. I am asking for the
official released version. As we can see the 4.5.5 is the one which was released
almost one year ago. Do you have any idea when the next version
Dear David:
If the two leaflets are moving with respect to each other (along the bilayer
plane), then why would this be artificial?
I have also seen this (diffusive) motion, and in addition to wondering why you
would call it artificial, it seems to me
that the motion would have to be many
The large magnitudes of orthogonal barriers in such systems will lead to both
systematic and statistical
sampling errors that motivate the application of both approaches, preferably
repeated a few times each.
So I think that Justin is right, in an idealized situation. I might modify his
I suggest that you post this to the VMD users list.
-- original message --
Dear All,
I just installed a VMD. And then I load a gro file and a xtc file from a
simulation. The bar in the VMD Main window continuously moves, however the
protein molecule in the OpenGL Display window does not
On 2012-08-14 08:52:26PM -0300, Sebastien Cote wrote:
Dear Peter,
I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm
(as in Klauda's paper). I will retry with a more solvated membrane.
Would you have any thought on how the NPAT ensemble might affect
The area per lipid (APL) will certainly affect the free energy of
peptide/protein binding to a lipid bilayer.
I have not used charmm lipids extensively, but from what I understand they
older charmm lipids required
NPAT to get the correct APL. The newer charmm lipids were supposed to solve
Thanks for the advices Chris.
My peptide is known to be more favorably to PE than PC membrane that is why I
am using POPE.
Experimentally, the liquid phase transition is at 298K for POPE (if I am not
mistaken). Is your 323K refer to some simulations?
At first I wanted to use the new
Write the authors of the simulation paper that has a correct APL for POPE and
ask them for an input file.
That is really the only way to be sure that you are not doing something
different than they did.
In my experience, people are quite willing to provide you with their input
file(s).
If you
On 2012-08-15 06:55:59PM +, Christopher Neale wrote:
Write the authors of the simulation paper that has a correct APL for POPE
and ask them for an input file.
That is really the only way to be sure that you are not doing something
different than they did.
In my experience, people are
Hi,
As I suggested earlier in this thread, I think the original poster
should run test simulations of a CHARMM36 POPE membrane using either the
NAMD or CHARMM softwares. It has been mentioned a couple of times in the
thread thay there are differences in the implementations of the
switching
Dear Gromacs users,
I am using gromacs for simulations of a polymer, for that I
am planing to see how lattice parameters a , b c are varying
during simulation. Here lattice parameter a is the length of unit
cell along X- direction, b is the length of the unit cell along
Y axis and c
Well, gromacs is not the only software available. I'd still ask them and then
try it in gromacs after parsing. \If there is a difference, then try in NAMD
and/or charmm. I know that this is the gromacs users list, but we're talking
about
debugging here and I think that getting the original
Hi,
I am a novice user of g_hbond (actually, I am using double precision --
g_hbond_d -- but I think all of the parameters should be the same).
I would like to use the output of the -hbn switch (which generates
hbond.ndx) in tandem with the -hbm switch (which generates an existence
matrix
Hi again,
I just looked at page 214 in the version 4.5.4 PDF manual (not the -h man
page), and it says:
An H-bond existence map can be generated of dimensions # H-bonds X #
frames. The ordering is identical to the index file (see below), but
reversed, meaning that the last triplet in the index
On 8/15/12 4:49 PM, Andrew DeYoung wrote:
Hi,
I am a novice user of g_hbond (actually, I am using double precision --
g_hbond_d -- but I think all of the parameters should be the same).
I would like to use the output of the -hbn switch (which generates
hbond.ndx) in tandem with the -hbm
On 8/15/12 4:54 PM, Andrew DeYoung wrote:
Hi again,
I just looked at page 214 in the version 4.5.4 PDF manual (not the -h man
page), and it says:
An H-bond existence map can be generated of dimensions # H-bonds X #
frames. The ordering is identical to the index file (see below), but
On 16/08/2012 5:46 AM, ramesh cheerla wrote:
Dear Gromacs users,
I am using gromacs for simulations of a polymer, for that I
am planing to see how lattice parameters a , b c are varying
during simulation. Here lattice parameter a is the length of unit
cell along X- direction, b
Thanks for the reply Mark,
I posted without thinking enough. In my workflow I have 10 ensembles. I sample
one frame of co-ordinates per ps at the end of my NPT equilibration and
generate new velocities for each of these frames. So they all have minor
variations in initial position and velocity.
Dear Mark,
Thank you for your reply, as you suggested I will go
through the sec 7.4 and 8 of the manual and moreover how would I get
exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of
trajectory in gromacs
As I am new to gromacs I have no Idea where these will be
On 16/08/2012 3:22 PM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, as you suggested I will go
through the sec 7.4 and 8 of the manual and moreover how would I get
exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of
trajectory in gromacs
They're in
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