On 19/08/2011 2:10 PM, bipin singh wrote:
Hello,
Please let me know from where can I get the full description of g_sham
module, as the manual does not
provide full description of the options for g_sham in gromacs.
for e.g I want to know the description about the following options in g_sham:
-map
Прочитайте вашего сообщение от Dmitriy Golubovsky или оно будет удалено!
Чтобы прочитать сообщение, перейдите по этой ссылке:
http://eu1.badoo.com/0205731908/in/JCdnCDIwImY/?lang_id=2&m=65&mid=4e4df17900023f097816
Еще некоторые из терпеливо ожидающих вас друзей:
Rasty James (Москва, Р
And I am happy to report that this method produces a viable starting
structure :)
On Thu, Aug 18, 2011 at 7:02 PM, Michael Daily wrote:
> I tried an experiment similar to yours - after converting the POPE's to
> POPC's when I remove all waters that are near the (lipid-emulsified)
> nanoparticle b
On 19/08/2011 1:41 PM, Junior Nebeker wrote:
Correct. Other people (who are new to this list) need your help, and
unless their requests are way out of line, there's no reason to adopt
a haughty attitude in responding.
There's never a case for rudeness, but when (for example) people have
been
Hello,
Please let me know from where can I get the full description of g_sham
module, as the manual does not
provide full description of the options for g_sham in gromacs.
for e.g I want to know the description about the following options in g_sham:
-map
-ls3
-mdata
--
---
R
Correct. Other people (who are new to this list) need your help, and unless
their requests are way out of line, there's no reason to adopt a haughty
attitude in responding.
On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham wrote:
> On 19/08/2011 9:32 AM, Junior Nebeker wrote:
>
>>
>> Hey mark,
>>
>>
I tried an experiment similar to yours - after converting the POPE's to
POPC's when I remove all waters that are near the (lipid-emulsified)
nanoparticle based on a radial criterion and then run genbox again, the
total number of waters decreases by about 1100. Compared to a control case
(ran genbo
It is true that on Intel CPUs with HT supported and on you get an up
to 10-15% speedup if you also use all virtual cores wrt to running
only as many threads as real cores. Additionally, as the OS reports
all virtual processors, by Gromacs will use all of them by default,
i.e. will run with 8 thread
Hi,
Gromacs 4.5.x works only with OpenMM 2.x. You might be able to use
CUDA 4.0, but you will probably have to recompile OpenMM from source.
Cheers,
--
Szilárd
On Fri, Aug 19, 2011 at 2:23 AM, Park, Jae Hyun nmn wrote:
> Dear GMX users,
>
>
>
> I am installing GMX 4.5.3 with GPU.
>
> But, the
Slightly off-topic, but for all but the smallest systems, I get a
further 10% efficiency by running a 16-process mpi job on an 8-core
machine. I suspect that the story is the same with threads. Thus, on a
16-core node, you could try starting 32 threads. Note that this will
report a 2x large
On 19/08/2011 9:32 AM, Junior Nebeker wrote:
Hey mark,
If you are really sick of asking people for such information, why do
you even care to respond to this mailing list?
Because I'd rather teach someone to fish than either give them fish or
watch them starve.
Mark
--
gmx-users mailing li
Indeed, gromacs (non-mpi) will use all the resources available. If you do not
want that you can control de number of threads created with the -nt option of
mdrun.
regards
Felipe
Mensaje original
De: wgal...@ualberta.ca
Fecha: 18-ago-2011 19:26
Para: "Discussion list for GROMACS user
It means you are running a lot of parallel processes, but that does not
translate into a linear increase in speed. So faster, but not 16X.
Warren Gallin
On 2011-08-18, at 5:36 PM, Park, Jae Hyun nmn wrote:
> Thank you, Warren.
> Does that mean 16 times faster ?
>
> Jae H. Park
>
> -Origi
Thank you, Warren.
Does that mean 16 times faster ?
Jae H. Park
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Warren Gallin
Sent: Thursday, August 18, 2011 7:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users]
Hey mark,
If you are really sick of asking people for such information, why do you
even care to respond to this mailing list?
On Thu, Aug 18, 2011 at 3:43 PM, Mark Abraham wrote:
> On 19/08/2011 1:22 AM, Nilesh Dhumal wrote:
>
>> Hello,
>>
>> How can I put constraints on an angle.
>>
>> I adde
Dear GMX users,
I am installing GMX 4.5.3 with GPU.
But, the CUDA in my GPU machine is ver 4.0. Can I use this version of CUDA and
openmm-3.1.1? Or, do I have to re-install CUDA 3.2 and openmm-2.0 as described
in manual?
Thank you in advance for your kind instruction.
Jae H. Park
I believe that the current version of GROMACS supports threading, which does
not require mpi.
So mdrun is running threads at 100% of the activity of each of your 16 nodes,
hence 1600%.
Warren Gallin
On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote:
> Hi GMX users,
>
> I installed GMX 4.5
Hi GMX users,
I installed GMX 4.5.3 recently.
But, when I just execute mdrun (without mpi, I did not installed mpi-version of
mdrun), the use of CPU appears more than 100% ("top" command in LINUX). How is
it possible?
For example, I am using 16-node machine. And if I simply run "mdrun", then us
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Monday, August 22, 2011.
For all questions about CloudBroker and the CloudBroker Platfor
On 19/08/2011 1:22 AM, Nilesh Dhumal wrote:
Hello,
How can I put constraints on an angle.
I added following lines in .top file
[ constraints ]
2 8 18 3 109.5
But its giving error.
Get in the habit of copying and pasting the error. Curiously enough, it
usually contains diagnostic in
Алексей Раевский wrote:
Hi. I need your help dealing with parametrization of mdp file. Look, I
want to understand how can we change such params like rlist, rvdw,
cut-off, rcoulomb. As I know each forcefield has its own properties and
calculated values of this params. But I've found that in di
Hi. I need your help dealing with parametrization of mdp file. Look, I want
to understand how can we change such params like rlist, rvdw, cut-off,
rcoulomb. As I know each forcefield has its own properties and calculated
values of this params. But I've found that in different articles this values
w
On Thu, Aug 18, 2011 at 3:02 PM, Justin A. Lemkul wrote:
>
>
> Roland Schulz wrote:
> > Hi,
> >
> > you can use trjconv for that (or editconf). You probably would want to
> > add some waters though.
> >
>
> For trjconv, you can get a coordinate file, but not a .cpt; editconf throws
> a
> fatal er
Roland Schulz wrote:
Hi,
you can use trjconv for that (or editconf). You probably would want to
add some waters though.
For trjconv, you can get a coordinate file, but not a .cpt; editconf throws a
fatal error (unless I'm using it wrong, but I tried -f state.cpt). If you try
to output
Hi,
you can use trjconv for that (or editconf). You probably would want to add
some waters though.
Roland
On Thu, Aug 18, 2011 at 2:50 PM, Peter C. Lai wrote:
> Is there anyway I can extract a subset of atoms from a cpt file, like I can
> with trjconv operating on a traj file? I want to remove
Peter C. Lai wrote:
Is there anyway I can extract a subset of atoms from a cpt file, like I can
with trjconv operating on a traj file? I want to remove a ligand and still
keep all the remainder of the state information, so I can feed this back
into grompp with a modified topology and "continue
Ye Yang wrote:
Oh, I see it now.
Even if I include all the needed terms in one file forcefield.itp, I
need to create files separated, using file name ffnonbonded.itp and
ffbonded.itp?
The #include keyword literally means "copy and paste the contents of this file
here." If those files don't
Is there anyway I can extract a subset of atoms from a cpt file, like I can
with trjconv operating on a traj file? I want to remove a ligand and still
keep all the remainder of the state information, so I can feed this back
into grompp with a modified topology and "continue" a run without the liga
Oh, I see it now.
Even if I include all the needed terms in one file forcefield.itp, I need to
create files separated, using file name ffnonbonded.itp and ffbonded.itp?
Thank you very much
Ye
2011/8/18 Justin A. Lemkul
>
>
> Ye Yang wrote:
>
>> Hi, Justin:
>> Thank you for the reply.
>>
Ye Yang wrote:
Hi, Justin:
Thank you for the reply.
But I am not sure for gromacs 4.5.4. since for gromacs 3.3.1, I
only need one itp file for my forcefield. Should I just split this
forcefield.itp file into two different part, and write a new
forcefield.itp which says "#include ff
Sara baretller wrote:
Hi justin
in the tutorail you have
It is not necessary to run a complete energy minimization procedure on
the bilayer, although you can if you want. The .tpr file contains
information about bonding and periodicity, so it can, in a sense, be
used to reconstruct "brok
Hi, Justin:
Thank you for the reply.
But I am not sure for gromacs 4.5.4. since for gromacs 3.3.1, I only
need one itp file for my forcefield. Should I just split this forcefield.itp
file into two different part, and write a new forcefield.itp which says
"#include ffnonbonded.itp, #includ
Hi justin
in the tutorail you have
It is not necessary to run a complete energy minimization procedure on the
bilayer, although you can if you want. The .tpr file contains information
about bonding and periodicity, so it can, in a sense, be used to reconstruct
"broken" molecules.
when i tried
My apologies; the remainder of the thread in which these suggestions
were already proposed and discussed showed up where I didn't expect
them. Sorry to repeat what's already been said.
MZ
On Thu, Aug 18, 2011 at 12:58 PM, Matthew Zwier wrote:
> Hi Itamar,
>
> In my experience, the 4.5 series ap
Ye Yang wrote:
Hi, everyone:
I am using a forcefield PACE(modified) from my friends.
Since there was a small program generating some dihedral terms
based on gromacs3.3.1, I need to use gromacs 3.3.1 to generate the
gromacs file.
Previously, for the npt/nvt, I was also using grom
Hi, everyone:
I am using a forcefield PACE(modified) from my friends.
Since there was a small program generating some dihedral terms based on
gromacs3.3.1, I need to use gromacs 3.3.1 to generate the gromacs file.
Previously, for the npt/nvt, I was also using grompp (gromacs 3.3.1) to
Hi Itamar,
In my experience, the 4.5 series appears to be slightly less tolerant
of unstable systems than the 4.0 series. Try minimizing and/or
equilibrating your system longer. See
http://www.gromacs.org/Documentation/Errors and
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
MZ
never mind , added both names and worked. did not work first time but then
it did
thank you
On Thu, Aug 18, 2011 at 12:00 PM, Sara baretller <
sarabiocomputat...@gmail.com> wrote:
>
>
> what do i write on the top of the system.gro file before the number of the
> molecules. do i add the name of p
what do i write on the top of the system.gro file before the number of the
molecules. do i add the name of protein and the name of bilayer or somthing
else to represent both systems in one system
Thank you
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinf
Hi Nilesh,
You can constrain the length between atoms A and C from a triple
A-B-C, provided AB and BC are also constraint.
Cheers,
Tsjerk
On Thu, Aug 18, 2011 at 5:22 PM, Nilesh Dhumal wrote:
> Hello,
>
> How can I put constraints on an angle.
>
> I added following lines in .top file
>
> [ c
Hello,
How can I put constraints on an angle.
I added following lines in .top file
[ constraints ]
2 8 18 3 109.5
But its giving error.
How can I put constraints on an angle.
I am using Gromacs 4.0.7 version.
Thanks
Nilesh
--
gmx-users mailing listgmx-users@groma
On 19/08/2011 12:43 AM, shikha nangia wrote:
Dear all:
I would like to create a smaller simulation box (from a larger
simulation box in .gro file) by removing atoms in the x, y and
z-directions and saving the subset system into a new .gro file
(smaller box and subset of molecules)
For examp
Dear all:
I would like to create a smaller simulation box (from a larger simulation box
in .gro file) by removing atoms in the x, y and z-directions and saving the
subset system into a new .gro file (smaller box and subset of molecules)
For example: from original box 10x10x10 nm3 write coordin
On Thu, 2011-08-18 at 15:44 +0200, Elton Carvalho wrote:
> On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal
> wrote:
> > Using g_velacc I can calculate the velocity autocorrelation function of a
> > group as a vector.
> >
> > Can I calculate the velocity autocorrelation function as a scalar?
>
On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal wrote:
> Using g_velacc I can calculate the velocity autocorrelation function of a
> group as a vector.
>
> Can I calculate the velocity autocorrelation function as a scalar?
My naïve suggestion would be to take the norm of that vector.
--
Elton C
I am using 24 processors and it is same for all steps.
this is the command in use:
tpbconv_mpi -f run.trr -s run.tpr -e run.edr -extend 1000 -o ext_11
nohup /opt/ScaleMP/mpich2/1.0.8/bin/mpirun -machinefile $PBS_NODEFILE -np 24
/opt/gromacs4/bin/mdrun_mpi -v -deffnm ext_11
-
On 18/08/11, Anupam Nath Jha wrote:
>
>
> Dear all
>
> I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes.
>
> I am writing log files for different ns (1-10) in different files i.e.
> different
> files for each nano second . The performance goes like following:
>
> ---
Dear all,
When I compile gromacs using cmake, no large file related option was found
in the cmake interface, however, I found the option for large file support
in the CMakeCache.txt listed as bellow.
.
//Result of TEST_BIG_ENDIAN
GMX_INTEGER_BIG_ENDIAN:INTERNAL=0
//Result of test for large fil
Dear all
I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes.
I am writing log files for different ns (1-10) in different files i.e. different
files for each nano second . The performance goes like following:
--
for 1st ns:
(Mnbf/s) (GFlops
Bert wrote:
Dear gmx-users,
When I continued a run on my x86_64 linux clusters using the command
"mdrun -deffnm prod -cpi prod.cpt -append", I got the errors as below:
Program mdrun, VERSION 4.5.4
Source code file: checkpoint.c, line: 1734
Fatal error:
The original run wrote a file called
On 18/08/11, Kavyashree M wrote:
> Its strange I get some mails, But Dr. Mark's reply for
> my previous mail I dint get. So I thought there is some
> problem.
Maybe you or your ISP have some spam filters that are over-zealous. Unless
there's more people observing problems, it seems unlike
Its strange I get some mails, But Dr. Mark's reply for
my previous mail I dint get. So I thought there is some
problem.
Thank you
With Regards
Kavya
On Thu, Aug 18, 2011 at 9:24 AM, Justin A. Lemkul wrote:
>
>
> Kavyashree M wrote:
>
>> Respected Sir,
>> I am not receiving reply mails to my gm
52 matches
Mail list logo
