Dear all,
if I compare GPU-accelerated and CPU-only runs, I get significantly different
results/energies with
Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no
difference between CPU-only runs and with GPU.
In short, with Gromacs 5.x using GPUs, I have lower total energy,
On Mon, Sep 22, 2014 at 9:44 AM, Machtens, Jan-Philipp
j.macht...@fz-juelich.de wrote:
Dear all,
if I compare GPU-accelerated and CPU-only runs, I get significantly
different results/energies with
Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no
difference between
Thanks for the reply!
However, the differences between GPU runs and CPU-only runs for
Gromacs 5.x that I observe are statistically significant (10-100 ns for each
test sim) (and reproducible).
In contrast, with Gromacs 4.6.x I do not have significant differences that
I can apparently attribute to
On Mon, Sep 22, 2014 at 11:02 AM, Machtens, Jan-Philipp
j.macht...@fz-juelich.de wrote:
Thanks for the reply!
However, the differences between GPU runs and CPU-only runs for
Gromacs 5.x that I observe are statistically significant (10-100 ns for
each test sim) (and reproducible).
In
Does anyone know that how to use NVIDIA Visual Profiler to profile gromacs-5.0?
xiexiao...@sjtu.edu.cn
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My goal, for now, is to model a polimer (nylon-6) chain, and to find the
equilibrium position of the chain considering the capacity to be rolled up
itself.
I had create a pdb file using Avogadro software, but when i go to gromacs to
input the data using the function pdb2gmx
And indipendently
Hi,
i had checked all the archives, i have read about 100posts in the last 2 month.
Nobody have problem similar to mine.
Problem for me are Two.
1- instead i am a doctor, i am not able to find the right advice at your site.
2- In your site there is no space for begginer user.
The main pages
Add the parameters for LIG residue in force filed. In that give information
about the LIG in
rtp file
nonbonded file
bonded file
I think then it will work.
On Mon, Sep 22, 2014 at 5:46 AM, marcello cammarata mstaxmarce...@yahoo.it
wrote:
Hi,
i had checked all the archives, i have read about
On 9/22/14 4:48 AM, Anurag Dobhal wrote:
I am getting an error while running the commmand
gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
Fatal error:
Unknown atomtype OW
please help !!!
You deleted a necessary atom type. Follow the instructions carefully and
On 9/22/14 8:46 AM, marcello cammarata wrote:
Hi,
i had checked all the archives, i have read about 100posts in the last 2
month.
Nobody have problem similar to mine.
Problem for me are Two.
1- instead i am a doctor, i am not able to find the right advice at your site.
2- In your site
On 9/22/14 3:00 AM, Anurag Dobhal wrote:
I have followed the following steps for installaing gromacs 5.0.1
tar xfz gromacs-5.0.1.tar.gz
cd gromacs-5.0.1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source
On 9/22/14 1:23 AM, RINU KHATTRI wrote:
hello justin
yes i did minimization and equilibrium
i have one confusion when i am going for extension of simulation by
tpbconv -s md_0_1.tpr -extend 9000 -o nextr.tpr
for mdrun i have to use which checkpoint file md_0_1.cpt after 1 ns or
state.cpt i am
Hi. I noticed mis-spellings in manual of another MD software that persisted
throughout its versions.
Googling for polyethylene simulation gave this article as first result:
http://arxiv.org/pdf/1401.4295v1.pdf, which use lammps.
I'm not sure about the availability, accuracy, and computation cost
hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
Command 'gcx' from package 'gcx' (universe)
On 9/22/14 10:14 AM, Yaser Hosseini wrote:
hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
The same way as you would use it with any other code. If you are not
familiar with the tools, I suggest you read the documentation; there
are tutorials available too e.g.
http://devblogs.nvidia.com/parallelforall/cuda-pro-tip-nvprof-your-handy-universal-gpu-profiler/
and there should be recorded
Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2 ps.
But it can be very slowly. Does anybody know how to do it more correctly?
2014-09-18 20:03 GMT+07:00 Tamas Karpati tkarp...@gmail.com:
Hello:
I just found a pretty nice free energy calculation methods: FEP MAPPER.
It can make a energy circle between different scalefold ligands which
improved a lot for the free energy values.
https://simtk.org/home/leadoptmap
I am just wondering, is it possible to do it in Gromacs?
Thank
Dear all,
I have carried out simulations of two homologous proteins (~38kDA) using
Gromacs v4.5.3 using OPLS force field. The protein consists of three
domains. Structural studies using cystallography reported earlier showed
that the two proteins differ in the extent of orientations one domain
On 9/22/14 10:45 AM, Александр Селютин wrote:
Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2 ps.
But it can be very slowly. Does anybody know how to do it more correctly?
I don't
On 9/22/14 2:26 PM, Anu Chandran wrote:
Dear all,
I have carried out simulations of two homologous proteins (~38kDA) using
Gromacs v4.5.3 using OPLS force field. The protein consists of three
domains. Structural studies using cystallography reported earlier showed
that the two proteins differ
On Mon, Sep 22, 2014 at 7:33 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/22/14 10:45 AM, Александр Селютин wrote:
Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2
ps.
But it
Additionally to Mark's comments, let me ask/add a couple of things.
What was your benchmarking procedure on core counts that represent
less than a full socket?
Besides the thread affinity issue mentioned by Mark, clock frequency
scaling (boost) can also distort performance plots. You will observe
Dear All,
I am trying to run NPT simulations using GROMACS version 5.0.1 of a system
of size 140k atoms (protein+water systems) with 2 or more GPU's
(model=k20); 8 cores (or more); and 1 or more nodes. I am trying to
understand how to run simulations using multiple gpus on more than one
node. I
Mark,
Thanks for sharing. Since the best way to write code that scales well is to
write code that runs slowly, we generally prefer to look at raw ns/day.
Choosing between perfect scaling of implementation A at 10 ns/day and
imperfect scaling of implementation B starting at 50 ns/day is a
Szilard, thanks for the comments and thoughts.
What was your benchmarking procedure on core counts that represent
less than a full socket?
As a starting point, I simply used the same settings for everything.
Besides the thread affinity issue mentioned by Mark, clock frequency
scaling
On Tue, Sep 23, 2014 at 1:32 AM, Dallas Warren dallas.war...@monash.edu
wrote:
Mark,
Thanks for sharing. Since the best way to write code that scales well is
to
write code that runs slowly, we generally prefer to look at raw ns/day.
Choosing between perfect scaling of implementation A at
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