Shi,
Justin straightened me out regarding the command structure ; Used "mpirun -np
8 gmx_mpi mdrun -deffnm Run_file.nvt”
But for time being I’ve given up on two GPUs with the 32 core system. I am now
just trying to make the single GPU work well.
Paul
> On Dec 19, 2018, at 5:51 AM, Shi Li
In addition to Justin’s comments, the repository version is not adapted to
GPU/CUDA use and as such is good for only very small systems and so loses one
of the great advantages over other MD programs. I is not bad as an introduction
to Gromacs so do not be afraid of installing, working with
Hi Justin,
Thank you very much.
On Tue, Dec 18, 2018 at 12:23 AM Justin Lemkul wrote:
> On Mon, Dec 17, 2018 at 1:49 AM Shan Jayasinghe <
> shanjayasinghe2...@gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> > How do we determine the epsilon_r for a MD simulation? If we do a MD
> > simulation
On Wed, Dec 19, 2018 at 6:58 PM Zhang Shenqiu
wrote:
> Dear Everyone,
>
> I am a beginner to Gromacs, and found Gromacs can be installed with
> apt-get install gromacs on Debian/Ubuntu. But I hesitate to use it because
> this option is not listed or mentioned in the installation guide.
> http://m
Dear Everyone,
I am a beginner to Gromacs, and found Gromacs can be installed with apt-get
install gromacs on Debian/Ubuntu. But I hesitate to use it because this option
is not listed or mentioned in the installation guide.
http://manual.gromacs.org/documentation/2018/install-guide/index.html
Good afternon.
How can i calculate th S2 order parameters???
Thanks.
Em qua, 19 de dez de 2018 às 11:51, Dr Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> escreveu:
> Hi Everyone,
>
> Is the S2max and S2min produced by gmx chi is same as Ss (slow order
> parameter)and Sf (fast order p
I've finallly got the ducks in order, The command
mpirun -np 8 gmx_mpi mdrun -deffnm PVP20k.nvt auto maps the process as:
On host xxx 2 GPUs auto-selected for this run.
Mapping of GPU IDs to the 8 GPU tasks in the 8 ranks on this node:
PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1
this for the 32 core
On Wed, Dec 19, 2018 at 4:34 AM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:
> Dear Sir,
>
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from
Getting closer...
( thinking a bit about the initial command structure does help)
Now using the command:
gmx_mpi mdrun -deffnm PVP20k.nvt -nb gpu -ntomp 16 -npme 4
:-) GROMACS - gmx mdrun, 2018.4 (-:
gets past the v5 issue but a new nastygram is sent...
"The -dd or -npme option request a para
Thank you - both - very much again.
The "mpir_run -npx gmx -mdrun." command was lifted from a Feb 2018
response from Szilard , to a multi gpu, user which he used as an example.
I'll crank on your pointers right now.
Paul
-Original Message-
From: gromacs.org_gmx-users-boun...@m
On Wed, Dec 19, 2018 at 11:44 AM p buscemi wrote:
> Shi,
>
> reinstalling the mpi version using gmx 18.4 did not helpany ideas ?
> hms@rgb2 ~/Desktop/PVP20k $ mpirun -np 8 mdrun_mpi -deffnm PVP20k1.em
> :-) GROMACS - mdrun_mpi, VERSION 5.1.2 (-:
>
>
You're just calling the same (incorrect
Shi,
reinstalling the mpi version using gmx 18.4 did not helpany ideas ?
hms@rgb2 ~/Desktop/PVP20k $ mpirun -np 8 mdrun_mpi -deffnm PVP20k1.em
:-) GROMACS - mdrun_mpi, VERSION 5.1.2 (-:
GROMACS: mdrun_mpi, VERSION 5.1.2
Executable: /usr/bin/mdrun_mpi.openmpi
Data prefix: /usr
Command line
here is the output from the gmx_mpi command. I would think the correct version
of mdrun would be installed. maybe I could point to it in my PATH ??
-
hms@rgb2 ~/Desktop/PVP20k $ gmx_mpi
:-) GROMACS - gmx_mpi, 2019
Hello,
A colleague of mine stumbled upon an issue with angles between 3 virtual
sites. If the 3 virtual sites are "Virtual Sites N", then the angle is
removed as being a constant-energy interaction. This can be prevented by
passing -normvsbds to grompp. Though, using the option is a workaround
Hi Everyone,
Is the S2max and S2min produced by gmx chi is same as Ss (slow order
parameter)and Sf (fast order parameter) respectively. If not may anybody
please explain what are those (S2max and S2min).
Thanks a lot.
Sincerely
Tushar
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>
>
> --
>
> Message: 3
> Date: Tue, 18 Dec 2018 21:51:41 -0600
> From: paul buscemi
> To: "gmx-us...@gromacs.org"
> Subject: Re: [gmx-users] error on opening gmx_mpi
> Message-ID:
> Content-Type: text/plain; charset=utf-8
>
> Shi, Thanks fo the note
>
> Yes
Hi,
> On 18. Dec 2018, at 18:04, Zachary Wehrspan wrote:
>
> Hello,
>
>
> I have a quick question about how GROMACs 2018.5 distributes GPU resources
> across multiple nodes all running one simulation. Reading the
> documentation, I think it says that only 1 GPU can be assigned to the PME
> cal
Hello,
I did a CGMD run of a membrane protein embedded in a model bilayer and I
want to compute the contacts between my protein and the PO4 beads of
certain lipid. I am using the following command:
gmx mindist -s md_protein_membrane_1.tpr -f
md_protein_membrane_centered_run1.xtc -or mindistr
Hi Shahee,
that's a nontrivial question ;)
It depends on what you call a contact; it probably has something to do
with the vdw radius of the CG beads. Either way, we can't answer that
question for you.
Peter
On 19-12-18 10:57, SHAHEE ISLAM wrote:
> hi,
> i am doing the contact between the all
hi,
i am doing the contact between the all backbone beads within a protein
by using the below command.
gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5
where -t is trunc distance.what value should i use for martini coarse
grained system because by changing -t value the plots are als
Hi Shahee,
what cutoff do you mean?
You can find sample Martini MDP files here:
http://cgmartini.nl/index.php/force-field-parameters/input-parameters.
The normal VDW and coulomb cutoffs are 1.1 nm.
Peter
On 19-12-18 09:30, SHAHEE ISLAM wrote:
> thank you so much for your reply.
> I have done
Dear Sir,
I am running GROMACS 5.1.4 on a server.
I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
As per your suggestion, I had downloaded the parameter files from ATB
server. As per the readme file from the server (in the parameters folder),
i had updated my topol.top lik
thank you so much for your reply.
I have done according your instruction.Can you please tell me what
should best cut off for martini coarse grained force field.
thanking you
shahee
On 12/18/18, soumadwip ghosh wrote:
> Hi,
>
> You can obtain the backbone atom contacts in the same protein using t
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