Dear gromacs users
I have Dppc monolayer on Tip4p2005 water layer.
I use gromacs 4.0.7, tcoupl=v-rescale
command line in .ll file:
mpiexec mdrun -v -s topol.tpr
(I have made topol.tpr with the following command:
grompp -c .gro -f .mdp -n .ndx -p .top -o .tpr
now submitting the .ll file with
Hello
Previously I used gromacs/3.3 for my simulations of DPPc monolayer+Tip4P2005. I
saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load imbalance.
with this version because of load
On 2011-04-13 11.26, delara aghaie wrote:
Hello
Previously I used gromacs/3.3 for my simulations of DPPc
monolayer+Tip4P2005. I saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load
delara aghaie skrev 2011-04-13 11.26:
Hello
Previously I used gromacs/3.3 for my simulations of DPPc
monolayer+Tip4P2005. I saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load
Dear Dr. van der Spoel
many thanks for your explanations.
I want to know how I can overcome the performance loss due to load imbalance?
Thanks
regards
Delara
--- On Wed, 4/13/11, David van der Spoel sp...@xray.bmc.uu.se wrote:
From: David van der Spoel sp...@xray.bmc.uu.se
Subject: Re:
Dear Erik
Thanks for your explanation :)
regards
Delara
--- On Wed, 4/13/11, Erik Marklund er...@xray.bmc.uu.se wrote:
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] 2nd question related to load imbalance
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date:
Hello
In version 4.0.7 in .ll file, I use command line:
mpiexec mdrun_mpi -v -s topol.tpr
I get error which does noe recognize mdrun_mpi
I change it to mdrun and it works.
1) is the bold command line ok?
2) version 4.0.7 does not need _mpi after commands?
thanks
D.Aghaie--
gmx-users mailing
delara aghaie wrote:
Hello
In version 4.0.7 in .ll file, I use command line:
*mpiexec mdrun_mpi -v -s topol.tpr*
I get error which does noe recognize mdrun_mpi
I change it to mdrun and it works.
1) is the bold command line ok?
Only if you have (1) compiled with MPI support and (2) named
Hello gmx-users !!
I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my systems. But the third system
should the memory problem. Below I have pasted my command and its output.
*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num
I missed my Gromacs version. It's 4.0.7
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury iitd...@gmail.comwrote:
Hello gmx-users !!
I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my
Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
position restrained md.
integrator = md
dt = 0.002
nsteps =
You can always try mdrun -dlb yes whch will turn on dynamic load balancing from
the beginning..
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of delara aghaie [d_agh...@yahoo.com]
Sent: Wednesday, April 13, 2011 4:41 AM
To:
Certain options require an amount of memory that is proportional to na x
nd x t, where na and nd are number of acceptors and donors, and t is
time. You need more memory. Or you could do your calculation for a
subset of your solvent.
Erik
Chandan Choudhury skrev 2011-04-13 13.29:
I missed my
On 13/04/2011 7:02 PM, delara aghaie wrote:
Dear gromacs users
I have Dppc monolayer on Tip4p2005 water layer.
I use gromacs 4.0.7, tcoupl=v-rescale
command line in .ll file:
mpiexec mdrun -v -s topol.tpr
(I have made topol.tpr with the following command:
*grompp -c .gro -f .mdp -n .ndx -p .top
Kavyashree M wrote:
Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
You're not doing NPT. You haven't specified pcoupl or any of the other relevant
Dear gmx-users,
I have performed further investigation on the subject of the velocity
distribution
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060316.html
and what I found looks like a sort of a bug to me. Namely, the velocity
distribution profiles are different if I simulate a
On 13/04/2011 10:01 PM, Mark Abraham wrote:
On 13/04/2011 7:02 PM, delara aghaie wrote:
Dear gromacs users
I have Dppc monolayer on Tip4p2005 water layer.
I use gromacs 4.0.7, tcoupl=v-rescale
command line in .ll file:
mpiexec mdrun -v -s topol.tpr
(I have made topol.tpr with the following
I am sorry I did not include it in the mail: i used the following:
pcoupl = Parrinello_Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
I agree that density of water is different depending on
Kavyashree M wrote:
I am sorry I did not include it in the mail: i used the following:
pcoupl = Parrinello_Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p
The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?
On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M
Kavyashree M wrote:
The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?
That's a 2.6% difference. I wouldn't call that nowhere close.
Ok Thanks.
On Wed, Apr 13, 2011 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this
Dear Gromacs Users,
I want to add a sphere of water molecules around a ligand. I know I need to
use -shell option in genbox. But first I I need to create a sphere. Please
could you guide me?
best,
Olga
--
gmx-users mailing listgmx-users@gromacs.org
Hi there
The amide partial charges in the share folder of gromacs G56A3ff is as
following
H H: +0.280 N: -0.280
| C: -0.380 O: -0.380
C-N-C-C other C : 0.000
O
I guess all protein people use
XUEMING TANG wrote:
Hi there
The amide partial charges in the share folder of gromacs G56A3ff is as
following
H H: +0.280 N: -0.280
| C: -0.380 O: -0.380
C-N-C-C other C : 0.000
O
I guess
Olga Ivchenko skrev 2011-04-13 15.20:
Dear Gromacs Users,
I want to add a sphere of water molecules around a ligand. I know I
need to use -shell option in genbox. But first I I need to create a
sphere. Please could you guide me?
best,
Olga
Just fill the box with water, then run trjorder
Hi,
You can try packmol (
http://www.ime.unicamp.br/~martinez/packmol/download.html) to create any
starting configuration of your interest. I found it very useful for random
initial configurations.
Hope this help.
Esteban Gabriel Vega Hissi
Área de Química Física
Departamento de Química
Hello,
I want to file a patch for g_hbond.
How can I do that.
Nilesh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post
Nilesh Dhumal wrote:
Hello,
I want to file a patch for g_hbond.
How can I do that.
Post a feature/enhancement request on redmine.gromacs.org.
-Justin
Nilesh
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Sent from my BlackBerry® wireless device
-Original Message-
From: Mark Abraham mark.abra...@anu.edu.au
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 13 Apr 2011 07:35:30
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users
Sent from my BlackBerry® wireless device
-Original Message-
From: Mark Abraham mark.abra...@anu.edu.au
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 13 Apr 2011 07:35:30
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users
Dear all,
I am trying to pull a metal out of the protein binding pocket following a
cavity in the protein structure. I followed the tutorial, but I find few
problems:
1) When the metal leaves the binding pocket, some ligands follow the
metal, even that I restrained the position of protein atoms
Jon Mujika wrote:
Dear all,
I am trying to pull a metal out of the protein binding pocket following
a cavity in the protein structure. I followed the tutorial, but I find
few problems:
1) When the metal leaves the binding pocket, some ligands follow the
metal, even that I restrained the
Hello everyone,
I have encountered a strange behavior while compressing a pure system.
I am applying 100 bar pressure with PME and it turned out that this pressure
leads to density of 20 SI. Changing PME to SHIFT compresses the system to
density of above 600 SI!! and I should add that PME and
Hello,
I am using g_enemat to calculate the energy matrix from the energy
file(edr file) and I am supplying Protein as a group in -groups
option.
The command I am supplied is as follows:
g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
energy.xvg -temp 328 -nocoul -nolj -nomean
but
bipin singh wrote:
Hello,
I am using g_enemat to calculate the energy matrix from the energy
file(edr file) and I am supplying Protein as a group in -groups
option.
The command I am supplied is as follows:
g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
energy.xvg -temp 328
Thanks for your reply
The following terms are present in my energy files
1 Angle2 Proper-Dih. 3 Improper-Dih.4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr.8 Coulomb-(SR)
9 Coul.-recip.10 Potential 11 Kinetic-En. 12
bipin singh wrote:
Thanks for your reply
The following terms are present in my energy files
1 Angle2 Proper-Dih. 3 Improper-Dih.4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr.8 Coulomb-(SR)
9 Coul.-recip.10 Potential 11
Hi,
This has been a long discussed question. But I am still not so clear after
reading some posts and papers.
What model should be used for OPLS-AA force field? Any consideration for the
choice? Is SPC/E a good one?
Michael shirts has said in
Jianhui Tian wrote:
Hi,
This has been a long discussed question. But I am still not so clear
after reading some posts and papers.
What model should be used for OPLS-AA force field? Any consideration for
the choice? Is SPC/E a good one?
Michael shirts has said in
On 14/04/2011 4:36 AM, Moeed wrote:
Hello everyone,
I have encountered a strange behavior while compressing a pure system.
I am applying 100 bar pressure with PME and it turned out that this
pressure leads to density of 20 SI. Changing PME to SHIFT compresses
the system to density of above
Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is
giving density of above 600SI (4.0.7) and the other density of
Dear Moeed,
You seem to be encountering same problem to mine, which was posted to this
list, .titled Unexpected results arising from T- and P-coupling methods. Some
gmxers responded it. You can look for and see them. I wish they can be helpful
to deal with your problem.
Chaofu Wu, Dr.
Hello,
If some part of molecule is outside the box. How Gromacs save the
coordinates in trajectory.
Nilesh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Nilesh Dhumal wrote:
Hello,
If some part of molecule is outside the box. How Gromacs save the
coordinates in trajectory.
There is no such thing as outside in a periodic system.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Nilesh
--
On 14/04/2011 10:22 AM, Moeed wrote:
Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density
of ~ 2 SI and box size is 15 nm), one with version 4.0.7 and the other
trial using 4.5.3. Both runs are almost equilibrated to 70 bar
pressure but one is giving density of above
On 13 April 2011 17:14, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/04/2011 4:36 AM, Moeed wrote:
Hello everyone,
I have encountered a strange behavior while compressing a pure system.
I am applying 100 bar pressure with PME and it turned out that this
pressure leads to density of
On 13 April 2011 18:45, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/04/2011 10:22 AM, Moeed wrote:
Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs are
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