On 22/08/2012 3:47 PM, Albert wrote:
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
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 i
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 tak
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 08/21/2012 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 someth
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 b
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 angle,dihedral,
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 betw
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 i
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 fe
Dear Jesmin,
On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan 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 Gromacs form t
On Mon, Aug 6, 2012 at 4:04 PM, ms 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 ../ -DGMX_OPENMM=O
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
http://www.gromacs.org/Documentation/Cut-off_schemes?highlight=verlet#How_to_u
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 i
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.
--
gmx-use
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
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
To: gmx-users@gromacs.org
Sent: Tuesday, August 21, 201
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
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 error
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 wrote:
Am 21.08.2012 18:22, schrieb gmx-use
Thanks Thomas.
Justin, could you please comment on this?
Steven
On Tue, Aug 21, 2012 at 5:37 PM, Thomas Schlesier wrote:
> Am 21.08.2012 18:22, schrieb gmx-users-requ...@gromacs.org:
>>
>> On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier
>> wrote:
>>>
>>> >Since your simulations of the individu
Am 21.08.2012 18:22, schrieb gmx-users-requ...@gromacs.org:
On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier 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 an
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 >=3
On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesier 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 should see no
> drift
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 also
On Tue, Aug 21, 2012 at 4:21 PM, Justin Lemkul wrote:
>
>
> On 8/21/12 11:18 AM, Steven Neumann wrote:
>>
>> On Tue, Aug 21, 2012 at 4:13 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul wrote:
>
On 8/21/12 11:18 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 4:13 PM, Justin Lemkul wrote:
On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul wrote:
On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see the example of the plot from US s
On Tue, Aug 21, 2012 at 4:13 PM, Justin Lemkul wrote:
>
>
> On 8/21/12 11:09 AM, Steven Neumann wrote:
>>
>> On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 8/21/12 10:42 AM, Steven Neumann wrote:
Please see the example of the plot from US simulations and W
On 8/21/12 11:09 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul 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 - thi
On Tue, Aug 21, 2012 at 3:48 PM, Justin Lemkul 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 grom
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
int
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
nst
On 8/21/12 10:23 AM, Steven Neumann wrote:
On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul 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
On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul 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 starti
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 co
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 guidance
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 [kcal/mol]
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 ad
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 t
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
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 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
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
(1
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 d
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 6:14 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
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 6:00 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 nam
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 equilbirat
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 f
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
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: [gmx-u
Sorry, please don't care about this email. I made a mistake here.
Thanks
Sincerely,
Shima
From: Shima Arasteh
To: Discussion list for GROMACS users
Sent: Tuesday, August 21, 2012 12:47 PM
Subject: [gmx-users] kalp15 in dppc and EM iteration
Dear users,
I'
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 cont
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 restrai
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 s
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