Hi,
This are all questions that mostly only you can answer.
On 18/08/15 12:42, anu chandra wrote:
Dear Gromcas users,
I am planning to do microsecond long simulation of membrane-protein system
and I have ~100,000 atoms in the systems. Since I am trying for microsecond
long simulations and I
Dear Gromcas users,
I am planning to do microsecond long simulation of membrane-protein system
and I have ~100,000 atoms in the systems. Since I am trying for microsecond
long simulations and I have a quiet large system, it can generate large
amount of data and in this regard I would like to
On 8/18/15 8:08 AM, anu chandra wrote:
Dear Gromcas users,
I just expericend an error while running mpi version of Gromcas on a 64
processors in a cluster. The command I used for running mdrun is as
follows,
mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2
But,
Dear Gromcas users,
I just expericend an error while running mpi version of Gromcas on a 64
processors in a cluster. The command I used for running mdrun is as
follows,
mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2
But, unfortunately the run terminated with following error
Dear all,
I have a question about the handling of the tabulated interactions.
I am using tabulated potentials for my simulations.
With grompp there is no problem, i.e. no error messages.
Running mdrun produces:
Fatal error:
A tabulated bond interaction table number 1 is out of the table
Hi Anu,
1) It really depends on what kind of analysis you are doing. If you are,
for example, studying bio-molecular interactions that take place over
microsecond long timescales then saving trajectories every 200-500 ps is
advisable. I myself do receptor-membrane atomistic simulations with a
Dear user,
I did umbrella sampling simulation and get PMF profile of my system.
In order to calculate the rate constant I need to estimate the transmission
coefficient.
Do you have any advice about getting the transmission coefficient in
GROMACS?
Best
--
Gromacs Users mailing list
* Please
Hi;
I've already converted topology and coordinate files which were generated with
amber tools to .gro format. But now, when I want to add 100Mm NaCl to the
system I get this error:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'c6m1_GMX.top'
For more
Dear Users,
Hi.
The system has about 3k atoms, and I used a rhombic dodecahedron box.
The node in the cluster has 2 sockets and 12 cores per socket. (24 sockets
in total)
It also has 4 gpu.
Will I waste cpu time, if I run with all 24 cores and assign 1 gpu to 3
cores?
Should I compile for
Hi gromacs users,
Our lab decides to buy some exclusive computational resources for MD
using gromacs. The HPC center in our university offers 2 options. I
guess some of you are using K80 GPU right now so I'd like to hear your
suggestions/experiences about it.
option 1 (Tesla K40):
* Dual Intel
Oh...
So you are using gnuplot? The gyrate.xvg file is xmgrace native, so if you want
to plot it with the built-in labels and such use xmgrace -nxy gyrate.xvg; if
you want to use gnuplot, then you need to have it filter out all of the lines
that have either # and @ symbols at the begining
Thanks Justin.
On Tue, Aug 18, 2015 at 1:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/18/15 8:08 AM, anu chandra wrote:
Dear Gromcas users,
I just expericend an error while running mpi version of Gromcas on a 64
processors in a cluster. The command I used for running mdrun is as
Yes, I'm using gnuplot. I'll give it a try and see if that works. Thanks!
2015-08-18 11:42 GMT-03:00 Smith, Micholas D. smit...@ornl.gov:
Oh...
So you are using gnuplot? The gyrate.xvg file is xmgrace native, so if you
want to plot it with the built-in labels and such use xmgrace -nxy
Hi;
I want to convert amber topology and coordinate files into gromacs topology
and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x
FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not
found
I've done the procedure mentioned in the website:
Hi,
I'm using same command but without gmx_mpi and it works.
On 18 Aug 2015 14:09, anu chandra anu80...@gmail.com wrote:
Dear Gromcas users,
I just expericend an error while running mpi version of Gromcas on a 64
processors in a cluster. The command I used for running mdrun is as
follows,
Many thanks for your suggestions.
On Tue, Aug 18, 2015 at 12:52 PM, Ganesh Shahane ganesh7shah...@gmail.com
wrote:
Hi Anu,
1) It really depends on what kind of analysis you are doing. If you are,
for example, studying bio-molecular interactions that take place over
microsecond long
Hi,
This is almost certainly a problem with simulation instability, so please
follow the approaches here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up to discover
more about what is wrong.
Mark
On Tue, Aug 18, 2015 at 3:09 PM Liz Bell lizb...@gmx.at wrote:
Dear all,
I have a
On 8/18/15 10:13 AM, Daniela Rivas wrote:
Micholas,
My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5.
One needs to specifically link against VMD's libraries when installing GROMACS
for reading non-GROMACS formats if you want to read, e.g. DCD.
-Justin
On 8/18/15 10:39 AM, Daniela Rivas wrote:
Since version 4.6 it is not necessary to do so, it detects it automatically
and it did. I didn't have problems obtaining the radius of gyration, I
actually have it. I just have problems getting the plot using the command:
plot gyrate.xvg using 1:2
Hi,
I've been trying to plot the radius of gyration I got using gromacs, but I
keep getting the segmentation fault. What does this mean? I have plenty
memory (32 TB), so it can't be a memory problem.
My trajectory has 4 frames (20 ns simulation) and I'm calculating the
radius of gyration of
Daniela,
What exact is your input? And what version of gromacs?
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From:
Daniela,
I believe your issue is the DCD file, as I look at the help for g_gyrate (from
4.6.5), I don't see a compatability with DCD. You could convert it to a pdb and
then using g_gyrate and see if that fixes the issue.
-Micholas
===
Micholas Dean Smith, PhD.
Post-doctoral
Micholas,
My input file is a DCD trajectory obtained in NAMD and I have gromacs 4.6.5.
2015-08-18 11:07 GMT-03:00 Smith, Micholas D. smit...@ornl.gov:
Daniela,
What exact is your input? And what version of gromacs?
===
Micholas Dean Smith, PhD.
Post-doctoral Research
Since version 4.6 it is not necessary to do so, it detects it automatically
and it did. I didn't have problems obtaining the radius of gyration, I
actually have it. I just have problems getting the plot using the command:
plot gyrate.xvg using 1:2 with lines
2015-08-18 11:23 GMT-03:00 Justin
So unless the file is corrupted or empty, this is a gnuplot problem and
not a gromacs one. Check inside your gyrate file with a text editor to
see if it is correct.
On 18/08/15 16:39, Daniela Rivas wrote:
Since version 4.6 it is not necessary to do so, it detects it automatically
and it did.
http://www.gromacs.org/Documentation/How-tos/Graphing_Data
On Tue, Aug 18, 2015 at 4:51 PM Daniela Rivas dani.riva...@gmail.com
wrote:
Yes, I'm using gnuplot. I'll give it a try and see if that works. Thanks!
2015-08-18 11:42 GMT-03:00 Smith, Micholas D. smit...@ornl.gov:
Oh...
So
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