Hi,
As I'm sure you know from reading up on membed, it works by scaling the
embedded protein to be tiny and turning off its interactions. The mostly
likely issue is that you didn't give those instructions correctly. Double
check the documentation, and use a recent version of GROMACS to get the bug
Hi,
You'll get a smooth life if your CUDA driver and runtime are both at least
as recent as your device. Your runtime is 8.0 in some cases, and the 384
driver is not very recent.
Mark
On Wed, Jan 9, 2019 at 1:58 AM paul buscemi wrote:
>
>
> > On Jan 8, 2019, at 6:29 PM, paul buscemi wrote:
>
Hi,
There's no reason it shouldn't work, but we don't test it. I have heard of
reports that setting thread affinity doesn't work with Cygwin, and that
will make mdrun slow.
Mark
On Wed, Jan 9, 2019 at 2:47 AM Neena Susan Eappen <
neena.susaneap...@mail.utoronto.ca> wrote:
> Thank you Wahab,
>
>
Hi,
If you have a heterogenous cluster and want optimal performance, then you
will need multiple GROMACS installations. Doing them on a network shared
filesystem and mounting the correct one for each machine is the way to be
efficient, but in some cases a local installation on each machine will
pe
Hi Shan,
I am not quite sure if you want to generate an REMD simulation mobility in
temperature space for the 30 replicas. If that be the case, then you can
use the data in the replica_temperature.xvg file to plot replica index vs
REMD steps. The 1st column in the file corresponds to the REMD steps
Hello,
I am trying to figure out how to run Replica Exchange with Solute Tempering
(REST2) simulation using CHARMM 36m force filed. The only method that I
found so far involves using Plumed (which would have worked for me).
However, the instructions I found (
https://plumed.github.io/doc-v2.4/user
Dear Gromacs users,
How do we plot a graph for temperature vs swap step number using a REMD
simulation with 30 systems. I already generated the replica_temp.xvg and
replica_index.xvg files using demux.pl script.
Thank you.
Best Regards
Shan Jayasinghe
--
Gromacs Users mailing list
* Please sea
Thank you Wahab,
Is there any issue with using Cygwin on Windows using GROMACS?
Neena
From: Neena Susan Eappen
Sent: Tuesday, January 8, 2019 4:07 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Shell platform for GROMACS on Windows?
He
> On Jan 8, 2019, at 6:29 PM, paul buscemi wrote:
>
> I just built from a similar situation but also went to Ubuntu Mint Tara 19 ,
> cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not
> install the driver from the toolkit -- add the 410 driver from the PPA) The
I just built from a similar situation but also went to Ubuntu Mint Tara 19 ,
cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not
install the driver from the toolkit ) added the 410 driver from the PPA and
the system is quite happy.
I believe I ran across some informa
Den 2019-01-08 kl. 20:33, skrev Adarsh V. K.:
Dear all,
recently upgraded Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04 with a new
GPU GTX1080TI. CUDA from 7.5 to 8. Driver 384.
Problem: GPU not detected during MD run. Details are as follows:
Try upgrading to gromacs 2019.
1) Running on 1 no
Dear all,
recently upgraded Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04 with a new
GPU GTX1080TI. CUDA from 7.5 to 8. Driver 384.
Problem: GPU not detected during MD run. Details are as follows:
1) Running on 1 node with total 8 cores, 8 logical cores, 0 compatible GPUs
Hardware detected:
But d
Hi,
We have few CentOS 7 servers that use the same application stack.
I compile Gromacs on one of them and I want to be able to run Gromacs from all
of them.
I run it from server that Gromacs not compile on it, I got:
Illegal instruction
What it the best way to install Gromacs for all of them?
hi,
i want to calculate interaction energy between two protein.
In my system there are two proteins,waters and ions.In my .mdp file
the, energygrps = PROTEIN W ION
i am using this command
gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg
then the following options are coming
1 B
On 08.01.2019 05:07, Neena Susan Eappen wrote:
> Hello GROMACS users,
> To run GROMACS on Windows OS, what is the best shell interface? Cygwin? or
> anything else?
On Windows, nowadays (Windows 10) GROMACS is either
compiled and run:
- as a native Windows program through the MS Visual Studio 2
Dear Gromacs users,
I would like to simulate a protein with a peptidic ligand. However the
ligand has modified amino acids such as a phosphothreonine, a naphthyl
alanine and a piperidine carboxylic acid. I am not familiar with modified
peptide so can anyone guide me toward some webserver such as
Hi All,
I have an aligned structure of protein+ligands in the membrane (a mixture
of DPPC and DOPC).
The structure is solvated with water (gmx solvate -cp
protein_ATP_membrane_box.gro -cs -o protein_ATP_membrane_box_solv.gro -p
topol1.top)
And I used it as input file for g_membed.
grompp_d -c prote
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