Dear:
I am going to calculate the area/lipids for my membane system and I
found that GridMAT for area/lipids calculation is not that reliable
since I calculate by XY/(0.5 lipids number) for the pure well
equilbirated POPC lipids system, my values is 67 which is close to
experimental data
On 21/08/2012 4:00 PM, Albert wrote:
Dear:
I am going to calculate the area/lipids for my membane system and I
found that GridMAT for area/lipids calculation is not that reliable
since I calculate by XY/(0.5 lipids number) for the pure well
equilbirated POPC lipids system, my values is 67
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: Tuesday, August 21, 2012 9:45 AM
Subject: Re: [gmx-users] parameters for output
Hi,
I have installed the developement version of GROMACS (4.6) that supports
multi-GPU. I am not able however to run it since conditions to use GPU are
quite complicated to me.
I was wondering then, if anyone could provide me with some input files that
would allow me to compare performance of
Dear users,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into is in 2. Pack the lipids around the protein step
After generating the new position restrain
Dear Gromacs users,
I am currently trying to get an expression of the energy of pi stacking
interactions (in DNA) and I would like to know how it is calculated in
Gromacs.
I guess that Gromacs is estimating the energy of the pi stacking as the
sum of the van Der Waals and electrostatics
Sorry, please don't care about this email. I made a mistake here.
Thanks
Sincerely,
Shima
From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, August 21, 2012 12:47 PM
Subject: [gmx-users]
Hi Mark,
Thanks for replying.
De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De
Mark Abraham [mark.abra...@anu.edu.au]
Enviado: segunda-feira, 20 de Agosto de 2012 0:23
Para: Discussion list for GROMACS users
Assunto: Re:
On 8/21/12 5:17 AM, Delmotte, Antoine wrote:
Dear Gromacs users,
I am currently trying to get an expression of the energy of pi stacking
interactions (in DNA) and I would like to know how it is calculated in Gromacs.
I guess that Gromacs is estimating the energy of the pi stacking as the sum
Dear All
I am trying to perform the azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp level which was
327 non-matching atom names
atom names from azide.top will be used
atom names
On 8/21/12 2:25 AM, Mark Abraham wrote:
On 21/08/2012 4:00 PM, Albert wrote:
Dear:
I am going to calculate the area/lipids for my membane system and I found
that GridMAT for area/lipids calculation is not that reliable since I
calculate by XY/(0.5 lipids number) for the pure well
On 8/21/12 6:00 AM, Deepak Ojha wrote:
Dear All
I am trying to perform the azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp level which was
327 non-matching atom names
atom
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into, is in 2. Pack the lipids around the protein
step.
After generating the new position restrain
On 8/21/12 6:14 AM, Shima Arasteh wrote:
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The problem I got stuck into, is in 2. Pack the lipids around the protein
step.
Allright, I will check the configurations of out and inputs to find out the
reason of warning.
Please let me know something:
Should I expect to see changes in area per lipids in each shrinking or it would
happen after 25th repeat suddenly?
Thanks .
Sincerely,
Shima
On 8/21/12 6:35 AM, Shima Arasteh wrote:
Allright, I will check the configurations of out and inputs to find out the
reason of warning.
Please let me know something:
Should I expect to see changes in area per lipids in each shrinking or it would
happen after 25th repeat suddenly?
It will
Thanks for your reply.
In order to check the warning of grompp after scaling up I ran grompp again
without -maxwarn:
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
WARNING 1 [file minim.mdp]:
The sum of the two largest charge group radii (3.840099) is larger than rlist
On 8/21/12 8:01 AM, Shima Arasteh wrote:
Thanks for your reply.
In order to check the warning of grompp after scaling up I ran grompp again
without -maxwarn:
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
WARNING 1 [file minim.mdp]:
The sum of the two largest charge
To remove the periodicity I ran the command trjconv -s em.tpr -f dppc128.gro
-o dppc128_whole.gro -pbc mol -ur compact and chose system .
Is removing the periodicity something other than this?
I don't have any idea to fix it here.:-(
It is just a way to repeat the tutorial from the begining!
On 8/21/12 9:24 AM, Shima Arasteh wrote:
To remove the periodicity I ran the command trjconv -s em.tpr -f dppc128.gro -o
dppc128_whole.gro -pbc mol -ur compact and chose system .
Is removing the periodicity something other than this?
That's the correct command. The differences between
Dear Gmx Users,
I got confused about reading free energy difference from PMF curve.
It is the difference between maximum value on PMF curve (plateau -
final state) and the starting point corresponding to minima.
So e.g. my curve starts at 0 [kcal/mol] going staright to minima of -2
kcal/mol and
Friends,
I have calculate the mean sq. displacement of water molecules in the first
hydration shell around the protein (distance of .25nm). I want to write the
code but i dnt know how to manipulate the coordinates to account for the
pbc. Any guidance from anyone would be a great help.
Thanks in
On 8/21/12 9:36 AM, Steven Neumann wrote:
Dear Gmx Users,
I got confused about reading free energy difference from PMF curve.
It is the difference between maximum value on PMF curve (plateau -
final state) and the starting point corresponding to minima.
So e.g. my curve starts at 0
On 8/21/12 10:01 AM, Bala subramanian wrote:
Friends,
I have calculate the mean sq. displacement of water molecules in the first
hydration shell around the protein (distance of .25nm). I want to write the
code but i dnt know how to manipulate the coordinates to account for the
pbc. Any
Hello,
I've done some googling, searched the website and mailing lists so
apologies in advance if this is a bothersome set of questions...
Long story short I'm trying to help make a gromacs user more efficient
by developing a better set of tools for interacting with both Platform
LSF and
On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 9:36 AM, Steven Neumann wrote:
Dear Gmx Users,
I got confused about reading free energy difference from PMF curve.
It is the difference between maximum value on PMF curve (plateau -
final state) and the
On 8/21/12 10:23 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 9:36 AM, Steven Neumann wrote:
Dear Gmx Users,
I got confused about reading free energy difference from PMF curve.
It is the difference between maximum value on PMF
Please see the example of the plot from US simulations and WHAM:
http://speedy.sh/Ecr3A/PMF.JPG
First grompp of frame 0 corresponds to 0.8 nm - this is what was shown
by grompp at the end.
The mdp file:
; Run parameters
define = -DPOSRES_T
integrator = md; leap-frog integrator
On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see the example of the plot from US simulations and WHAM:
http://speedy.sh/Ecr3A/PMF.JPG
First grompp of frame 0 corresponds to 0.8 nm - this is what was shown
by grompp at the end.
The mdp file:
; Run parameters
define = -DPOSRES_T
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see the example of the plot from US simulations and WHAM:
http://speedy.sh/Ecr3A/PMF.JPG
First grompp of frame 0 corresponds to 0.8 nm - this is what was shown
by
On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see the example of the plot from US simulations and WHAM:
http://speedy.sh/Ecr3A/PMF.JPG
First grompp of frame 0 corresponds
On Tue, Aug 21, 2012 at 4:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see the example of the plot from US simulations and
On 8/21/12 11:18 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 4:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see
On Tue, Aug 21, 2012 at 4:21 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 11:18 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 4:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul
Since your simulations of the individual windows are about 50 ns, you
could first dismiss the first 10 ns for equilibration, and then perform
the WHAM analysis for 10-30 ns and 30-50 ns. If everything is fine, you
should see no drift.
If you want to have more data for the analysis you could
On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier schl...@uni-mainz.de wrote:
Since your simulations of the individual windows are about 50 ns, you could
first dismiss the first 10 ns for equilibration, and then perform the WHAM
analysis for 10-30 ns and 30-50 ns. If everything is fine, you
Dear All,
I have installed gromacs 4.5.3 on a cluster. I downloaded the
gromacs-4.5-GPU-beta2-X86_64 binaries and followed the following
instructions:
* INSTALLING FROM BINARY DISTRIBUTION:
0. Prerequisites:
- OpenMM (included in the binary release)
- NVIDIA CUDA libraries (version
Am 21.08.2012 18:22, schrieb gmx-users-requ...@gromacs.org:
On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesierschl...@uni-mainz.de wrote:
Since your simulations of the individual windows are about 50 ns, you could
first dismiss the first 10 ns for equilibration, and then perform the WHAM
Thanks Thomas.
Justin, could you please comment on this?
Steven
On Tue, Aug 21, 2012 at 5:37 PM, Thomas Schlesier schl...@uni-mainz.de wrote:
Am 21.08.2012 18:22, schrieb gmx-users-requ...@gromacs.org:
On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesierschl...@uni-mainz.de
wrote:
Since your
On 8/21/12 12:46 PM, Steven Neumann wrote:
Thanks Thomas.
Justin, could you please comment on this?
I agree with everything Thomas has said. There's not really anything to say.
-Justin
Steven
On Tue, Aug 21, 2012 at 5:37 PM, Thomas Schlesier schl...@uni-mainz.de wrote:
Am 21.08.2012
Hi everyone; I am running a MD simulation of a 40 kDa protein bound to ADP in
GROMACS VERSION 4.5.5. I made three minimization with restrains in protein,
backbone and c-alpha, in that order, and two equilibration with 150 and 300K
using backbone restrains. But when I run my md I get this
On 8/21/12 12:59 PM, virginia miguel wrote:
Hi everyone; I am running a MD simulation of a 40 kDa protein bound to ADP in
GROMACS VERSION 4.5.5. I made three minimization with restrains in protein,
backbone and c-alpha, in that order, and two equilibration with 150 and 300K
using backbone
I visualized the dppc128.gro and dppc128_whole.gro. The dppc seems to get
smaller and more compact in dppc128_whole.gro than the dppc128.gro.
I think it's normal!
Sincerely,
Shima
From: Justin Lemkul jalem...@vt.edu
To: gmx-users@gromacs.org
Sent:
Dear All,
I am using AMBER94 force-field for my protein. In the original force
field paper the dihedral functional form has been given as (V/2)[ 1 +
cos(nPhi - gamma)] but in GROMACS(4.5.4) manual I see the (1/2)
factor is not there [ eq 4.62]. So is this internally handled in
GROMACS or should
Hello:
I found that recently both Amber and CHARMM FF have been updated
including CHARMM 37 (or so called c36_aug12 ?)
http://mackerell.umaryland.edu/CHARMM_ff_params.html , Amber 12SB, Amber
Lipid FF. Does anybody when those dedicated FF could be avaible in Gromacs?
THX
best
A.
--
On 8/21/12 2:20 PM, Albert wrote:
Hello:
I found that recently both Amber and CHARMM FF have been updated including
CHARMM 37 (or so called c36_aug12 ?)
http://mackerell.umaryland.edu/CHARMM_ff_params.html , Amber 12SB, Amber Lipid
FF. Does anybody when those dedicated FF could be avaible
Hi,
The short answer is that you need to turn on the new verlet cut-off scheme.
You read the following wiki pages:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration
On Mon, Aug 6, 2012 at 4:04 PM, ms deviceran...@gmail.com wrote:
Hi,
I am trying to compile Gromacs 4.5.5 with GPU support on Linux. I have
performed the following steps:
export OPENMM_ROOT_DIR=/home//gromacs/OpenMM2.0-Linux64/
mkdir build-gpu
mkdir exec-gpu
cd build-gpu
cmake ../
Dear Jesmin,
On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan shraba...@gmail.com wrote:
Dear All,
I have installed gromacs 4.5.3 on a cluster. I downloaded the
gromacs-4.5-GPU-beta2-X86_64 binaries and followed the following
instructions:
Those binaries are extremely outdated. Please compile
Dear Szilárd
I have downloaded Gromacs 4.6 from git. But I saw that implicit
solvent feature is still not supported.
Features currently not supported by the new GPU and SSE kernels:
Implicit solvent (but this will still be supported on the GPU through OpenMM)
But I need the implicit solvent
On 22/08/2012 3:33 AM, tarak karmakar wrote:
Dear All,
I am using AMBER94 force-field for my protein. In the original force
field paper the dihedral functional form has been given as (V/2)[ 1 +
cos(nPhi - gamma)] but in GROMACS(4.5.4) manual I see the (1/2)
factor is not there [ eq 4.62]. So
Hi all,
I want to prepare a basic elastic network model (tirion
model) of protein. For this i have taken only C-alpha atoms of the
protein
and considered only streching potential(k.(b-b0)^2)) and removed
rest of angle,dihedral,non bonded interactions. I have mentioned a
bond
On 22/08/2012 1:06 PM, mohan maruthi sena wrote:
Hi all,
I want to prepare a basic elastic network model (tirion
model) of protein. For this i have taken only C-alpha atoms of the
protein
and considered only streching potential(k.(b-b0)^2)) and removed
rest of
HI Justin
thanks for kind reply. Unfortunately I am didn't go that deep of the
FF and probably I am not so qualified for this job. So, I will wait a
little for then.
best
A
On 08/21/2012 08:25 PM, Justin Lemkul wrote:
On 8/21/12 2:20 PM, Albert wrote:
Hello:
I found that recently
On 08/21/2012 08:25 AM, Mark Abraham wrote:
Since that calculation is one of the main purposes of GridMAT, I'd
suspect you're comparing two different quantities, or not calculating
one correctly.
Mark
--
I am very curious about this. The initial ALP for my equilibrated POPC
system is
On 22/08/2012 3:34 PM, Albert wrote:
On 08/21/2012 08:25 AM, Mark Abraham wrote:
Since that calculation is one of the main purposes of GridMAT, I'd
suspect you're comparing two different quantities, or not calculating
one correctly.
Mark
--
I am very curious about this. The initial ALP for
On 08/22/2012 07:44 AM, Mark Abraham wrote:
I don't see how this relates to your claim that you computed a value
with GridMAT that doesn't relate to a value computed some other way.
Mark
HI Mark:
thanks for kind reply.
here is my parameter for for calculation. The vector values was
On 08/22/2012 07:44 AM, Mark Abraham wrote:
I don't see how this relates to your claim that you computed a value
with GridMAT that doesn't relate to a value computed some other way.
Mark
And here is the results. As we can see The values is really low.
However, when I visulizaed the system
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