I've run protein adsorptions on PE, PEO, nylon and the like. The way I approach
such models is to first model the surface. Depending on if you want an
"extruded" polymer or a cast surface will define how you restrain it. For most
of my models - polymer strands of about 1000 atoms, and using
Dear Users,
I often use Gromos force field because ATB provides top files for reasonably
large molecules - 1000 atoms. With Gromacs 2019.3 the error now appears:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off.
Dear Users,
I am getting reasonable performance from two rtx -2080ti's - AMD 32 core and on
another node two gtx-1080 ti's -AMD 16 core i.e 20-30 ns/day with 30 atoms.
But in all my runs the % usage of the gpu's is typcially 40% to 60 % . Given
that it is specialized software, I notice
***
gen-temp = 200
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On Jun 5 2019, at 12:48 pm, p buscemi wrote
Armenio,
I've used GTX 1060, 1070,1080 and RTX 2080. The RTX 2070 should also be
compatible. The problem may lie in the build.
Paul
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Dear Users,
I've been trying to solve this for several days. A box with 100 polymer strands
restrained in only the x direction on either end is built and under nvt the
strands will coalesce into groups of 8-15 molecules. Under npt isotropic or
semiisotropic or surface-tension, the box will
for work
On May 22 2019, at 12:08 pm, Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> Hi
> You can use gmx genrestr tool to create restrain .itp file for any set
> of atoms
>
> On Wed 22 May, 2019, 8:12 PM p buscemi, wrote:
> >
> > Dear Users,
>
Dear Users,
In using restrain files, I place the restraint itp in a separated directory in
which there may be other restraint files.
I notice that within the restraint itp there is no specific reference to the
molecule used to create the itp. I've run into an instance in which other than
the
Dear Users,
In using:
gmx density -f lipid.nvt.trr -s octanoate.nvt3.tpr -dens charge -center -symm
-sl 100 -b 4 -e 4.5
it appears that the average charge density of all frames and the total box size
is used in the calculation. Is there a way to
1) specify multiple ranges to output say, every
Dear users,
I've run a water membrane model through minimization, nvt, and npt with
pressure coupling = surface tension with compression 4.5e-5 4 0 and with 4.5e-5
4.5e-5. I wanted to increase the box size in the z direction to created an air
( really vacuum ) interface. The membrane is in the
Deaer Users,
I've gotten the apparently common error
"particles communicated to PME rank 19 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated."
but with a twist. The 5 ns npt
when you open a new terminal you need to run " source" again, but you probably
know this by now
or
add the path to your /etc/.profile to make the change permanent
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Dear Users,
I've performed an adsorption experiment in which a fraction of molecules in
solution adsorb to a surface. I can extract the index of those adsorbed, and I
can obtain the total interaction ( LJ ) of the energy group with the surface.
I can estimate the average interaction of the
Mirco, to continue the results from the 32 core AMD Ryzen 1080ti
8.4 % of the available CPU time was lost due to load imbalance in the domain
decomposition.
Core t (s) Wall t (s) (%)
Time: 151131.597 2361.432 6400.0
39:21
(ns/day) (hour/ns)
Performance: 7.318 3.280
command gmx mdrun -deffnm
core 2990 AMD TR. DLB is taking some time and I will be tuning
the system today. but it works. Results for 80k atoms will be reported.
Thank you all.
Paul
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On Dec 19 2018, at 11:36 am, p buscemi wrote:
> Gett
ters right now.
> Paul
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> On Behalf Of Justin
> Lemkul
> Sent: Wednesday, December 19, 2018 10:47 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] error on opening gmx_mpi
, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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On Dec 19 2018, at 10:04 am, p buscemi wrote:
> here is the output from the gmx_mpi command. I would think the correct
> v
rom. it may be easier purge
> everything and start again.
> Paul
> > On Dec 18, 2018, at 8:48 PM, Shi Li wrote:
> > >
> > > Message: 3
> > > Date: Tue, 18 Dec 2018 15:12:00 -0600
> > > From: p buscemi
> > > To: "=?utf-8?Q?gmx-use
I installed 2019 beata gmx_mpi with:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
-DCMAKE_CXX_COMPILER=/usr/bin/g++-7 -DCMAKE_C_COMPILER=/usr/bin/gcc-7
-DGMX_MPI=ON -DGMX_USE_OPENCL=ON
The install completed with no errors.
I need to take this step by step: in
Carsten
thanks for the suggestion.
Is it necessary to use the MPI version for gromacs when using multdir? - now
have the single node version loaded.
I'm hammering out the first 2080ti with the 32 core AMD. results are not
stellar. slower than an intel 17-7000 But I'll beat on it some more
Thank you, Mark, for the prompt response. I realize the limitations of the
system ( its over 8 yo ), but I did not expect the speed to decrease by 50%
with 12 available threads ! No combination of ntomp, ntmpi could raise ns/day
above 4 with two GPU, vs 6 with one GPU.
This is actually a
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