Hi Jonathan,
I suspect the dash is not of the right kind. Did you by chance copy/paste
the command? Did you try typing it?
Cheers,
Tsjerk
On Sat, Jul 13, 2013 at 12:03 AM, Jonathan Saboury wrote:
> I am following "Tutorial 1" from
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.
Hi all GROMACS users,
I need to make a pdb file of AOT reverse micell . Please some body tell me how
do I build it and which package would best for this work. Now I am using
PACKMOL but it seems just a geometrical mathematical manipulation. I want to
arrange charge, LJ parameter, hydrogen bond
Hi GROMACS users,
Could you please somebody tell me how do I solvate A Reverse Micell by fixed
(200) molecule of water keeping in fixed annular region around it. That is how
do I solvate spherical micell by water so that the width of spherical region
around it is fixed?
lots of thanks for help
On 2013-07-12 20:00, Mark Abraham wrote:
On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
Hi!
On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
It balances the total number of processes across all allocated nodes.
OK, but using it means you are hostage to its assumptions
I am following "Tutorial 1" from
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html
I try the command "editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro"
but I get the error:
"Program editconf, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, l
Hello all,
Is it possible one can calculate molecular diffusion of multi-component
systems in the gas phase by GROMACS?
This quantity is very important in evaporation of fluids when liquid and
vapour phases are in quasi-equilibrium state.
Any help would be highly appreciated?
Best
Rasoul
--
gm
Hello,
I am trying to run the qm-mm gas phase calculations for my system.
I am using following in md.mdp file.
title = cpeptide MD
cpp = /usr/bin/cpp
integrator = md
dt = 0.001; ps !
nsteps = 500 ; total 5 ps.
On 7/12/13 2:28 PM, Shima Arasteh wrote:
Thanks for your replies. :-)
So, if I want to the ion move in only z-direction, I need to set the 'pull_dim'
Y Y N? Correct?
But in tutorial Justin writes : pull_dim = N N Y: we are pulling only in the z-dimension. Thus, x
and y are set to "no" (N) a
Thanks for your replies. :-)
So, if I want to the ion move in only z-direction, I need to set the 'pull_dim'
Y Y N? Correct?
But in tutorial Justin writes : pull_dim = N N Y: we are pulling only in the
z-dimension. Thus, x and y are set to "no" (N) and z is set to "yes" (Y).
So what should I d
Hi,
To support an upcoming promotional video being prepared by the CRESTA
project (http://cresta-project.eu) which provides some of the funding
support for GROMACS development, it would be nice to have some
real-life examples of work being done with GROMACS as the visual
element while a voice-over
On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
> Hi!
>
> On 2013-07-12 11:15, Mark Abraham wrote:
>>
>> What does --loadbalance do?
>
>
> It balances the total number of processes across all allocated nodes.
OK, but using it means you are hostage to its assumptions about balance.
> The
> thing is
In GROMACS groups are called via the *.ndx file (default: index.ndx)
Be aware that 'pull_dim' determines in which diretions (x,y,z) the
umbrella potential acts. So use N N Y , if you want that the ion can
move freely (onsidering the pull) in the xy-plane and Y Y Y if you want
to also restrit th
Yes, I got Thomas response and I am so grateful in this about. :-)
Also many many thanks for your response Justin.
Although I don't know the definition of pull-vec yet and I need to study in
this about, Would you please let me know if the grompp knows what I wrote as
the COM of protein or not?
Hi!
On 2013-07-12 07:58, Shine A wrote:
Hi Sir,
Is it possible to run an REMD simulation having 16 replicas
in a
cluster(group of cpu) having 8 nodes. Here each node have 8
processors.
It is possible. If you have Gromacs (version >= 4.6) compiled with MPI
and you specify the numbe
On 7/12/13 11:32 AM, Shima Arasteh wrote:
Allright.
As I said earlier, my system is a lipid bilayer. A channel is inserted in it
and I want to run US on this system.
An ion is considered in center of the each window, the reaction coordinate is
set to z, so the group which is pulled is an
On 12/07/13 13:26, Francesco wrote:
Hi all,
I'm working with a 200K atoms system (protein + explicit water) and
after a while using a cpu cluster I had to switch to a gpu cluster.
I read both Acceleration and parallelization and Gromacs-gpu
documentation pages
(http://www.gromacs.org/Documentat
Allright.
As I said earlier, my system is a lipid bilayer. A channel is inserted in it
and I want to run US on this system.
An ion is considered in center of the each window, the reaction coordinate is
set to z, so the group which is pulled is an ion, and my ref group would be
COM of the pr
Hi!
On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
It balances the total number of processes across all allocated nodes.
The thing is that mpiexec does not know that I want each replica to fork
to 4 OpenMP threads. Thus, without this option and without affinities
(in a
Thanks a lot Mark, that worked (after I did "setenv LD_LIBRARY_PATH
${LD_LIBRARY_PATH}:/usr/people/douglas/programs/gromacs-4.6.3/install/lib").
Quoting Mark Abraham on Fri, 12 Jul 2013
13:22:01 +0100:
On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston
wrote:
Hi,
I am having trouble in
On 7/12/13 9:34 AM, maggin wrote:
I use pdb to do test :
catdcd -o 1dx0.gro 1dx0.pdb
error:
CatDCD 4.0
dcdplugin) unrecognized DCD header:
dcdplugin) [0]: 1380273473 [1]: 538987346
dcdplugin) [0]: 0x52454d41 [1]: 0x20204b52
dcdplugin) read_dcdheader: corruption or unrecognized fi
I use pdb to do test :
catdcd -o 1dx0.gro 1dx0.pdb
error:
CatDCD 4.0
dcdplugin) unrecognized DCD header:
dcdplugin) [0]: 1380273473 [1]: 538987346
dcdplugin) [0]: 0x52454d41 [1]: 0x20204b52
dcdplugin) read_dcdheader: corruption or unrecognized file structure
Error: could not open file
at redhat INUXAMD64
use:
catdcd -o md_0_1.xyz md_0_1.xtc
error:
CatDCD 4.0
dcdplugin) unrecognized DCD header:
dcdplugin) [0]: 1995 [1]: 1059782656
dcdplugin) [0]: 0x07cb [1]: 0x3f2b
dcdplugin) read_dcdheader: corruption or unrecognized file structure
Error: could not open
at linux --- ubantu:
use:
catdcd -o md_0_1.xyz md_0_1.xtc
error:
CatDCD 4.0
dcdplugin) unrecognized DCD header:
dcdplugin) [0]: 1995 [1]: 1059782656
dcdplugin) [0]: 0x07cb [1]: 0x3f2b
dcdplugin) read_dcdheader: corruption or unrecognized file structure
Error: could not open
Hi all,
I'm working with a 200K atoms system (protein + explicit water) and
after a while using a cpu cluster I had to switch to a gpu cluster.
I read both Acceleration and parallelization and Gromacs-gpu
documentation pages
(http://www.gromacs.org/Documentation/Acceleration_and_parallelization
and
On Fri, Jul 12, 2013 at 11:18 AM, Douglas Houston
wrote:
> Hi,
>
> I am having trouble installing Gromacs 4.6.3.
>
> In bash I am using the following sequence of commands:
>
> cd gromacs-4.6.3
> mkdir build
> cd build
> CC=/usr/people/douglas/programs/gcc-4.7.3/installation/bin/gcc
> ~/programs/cm
Yes, Google knows quite a lot about this question! Please search before asking.
Mark
On Fri, Jul 12, 2013 at 11:43 AM, maggin wrote:
> Hi,
>
> Is anybody known how to convert gromacs formats and xyz?
>
> If VMD or catdcd can do it ?
>
> Thank you very much!
>
> maggin
>
>
>
>
>
> --
> View this
Hi,
Is anybody known how to convert gromacs formats and xyz?
If VMD or catdcd can do it ?
Thank you very much!
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/convert-gromacs-formats-and-xyz-tp5009793.html
Sent from the GROMACS Users Forum mailing list archive at
Hi,
I am having trouble installing Gromacs 4.6.3.
In bash I am using the following sequence of commands:
cd gromacs-4.6.3
mkdir build
cd build
CC=/usr/people/douglas/programs/gcc-4.7.3/installation/bin/gcc
~/programs/cmake-2.8.7/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
make
sudo make install
Ev
But you need each of these lines for both cases (SMD and US). Probably
one could skip two lines and use the default values, but it's better to
set them manually. See below for comments (comments are under the
related entry):
Thanks for your reply. But when I don't understand why these extra
Allright.
As I said earlier, my system is a lipid bilayer. A channel is inserted in it
and I want to run US on this system.
An ion is considered in center of the each window, the reaction coordinate is
set to z, so the group which is pulled is an ion, and my ref group would be
COM of the prote
On Thu, Jul 11, 2013 at 11:41 PM, Neha wrote:
>
>
> The .cpt file stores information related to output frequency. The existing
> .cpt
> file designates output every X steps, while the new .tpr file specifies
> output
> every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at
>
What does --loadbalance do? What do the .log files say about
OMP_NUM_THREADS, thread affinities, pinning, etc?
Mark
On Fri, Jul 12, 2013 at 3:46 AM, gigo wrote:
> Dear GMXers,
> With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
> separate MPI jobs of course (OpenMPI 1.6.4).
Hi,
We will have AVX2 acceleration ready for general usage before the end of July
(together with some other goodies), and it will be markedly faster, but until
it's ready and tested to give correct results we can't say anything about the
final performance.
However, in general AVX2 will have th
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