Hello users,
I know there are lots of discussion on this topic and i have gone through
all those even whole chapter 5 also. but didn’t get any solution or where i
am wrong. i want to generate .tpr file. i am using gmx grompp -f ions.mdp
-c solv.gro -p topol.top -o ions.tpr. in that i have
Hi,
What compiler are you using? Please also paste the output of "gmx -version".
Roland
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> David Lister
> Sent: Thursday, January 31,
Hello,
I've compiled gromacs 2018.5 in double precision a couple times now and it
keeps on failing the same tests every time. This is on Ubuntu 18.04 with an
i9 7900X.
The cmake I used was:
cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_BUILD_TYPE=Release
Sorry, that's 32 GB of RAM. I'm old, a MB used to be a lot of memory!
Mike
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Moir, Michael
(MMoir)
Sent: Thursday, January 31, 2019 6:29 PM
To: 'gmx-us...@gromacs.org'
Subject: [**EXTERNAL**] Re:
Stephano,
With a motherboard that doesn't split the PCI-E bandwidth, I get a 20%
improvement in computation speed with 2 GPUs. Whether or not you think this is
worth the extra $, I leave that up to you! My system is: i9-9900K, ASUS WS
Z390 Pro motherboard, 2x 1070ti GPUs, 32 MB 3200 MHz
Hi,
I have the simulation trajectory of a protein. I want to examine the bonded
as well as non-bonded energy for a contiguous set of backbone atoms in the
protein, say starting from C-alpha atom of residue i to C-alpha atom of
residue i+2. I saw that there is an option in the mdp file called
Stefano,
I'm investigating that myself. If your motherboard splits the bandwidth
between your PCI-E slots then there is no advantage to having 2 GPUs for a GPU
like the 1080. I have just upgraded to a better motherboard that does not
split the bandwidth but I am not finished my testing.
I performed MD for apoprotein after this I want to calculate potential
energy or short-range and long-range energy and enthalpy "per residue"
please help me how can I do this?
--
Gromacs Users mailing list
* Please search the archive at
Dear all,
I am tryin to set a new workstation and I would like to know if there is a
significant improvement in performance with two gpus (gtx 1080 ti or rtx
2080) rather than just one, and eventually with which cpu/ram requisite.
Thanks in advance for any advice and suggestions
Stefano
--
On Thu, Jan 31, 2019 at 2:14 PM Szilárd Páll wrote:
>
> On Wed, Jan 30, 2019 at 5:15 PM Tafelmeier, Stefanie
> wrote:
> >
> > Dear all,
> >
> > We are facing an issue with the CUDA toolkit.
> > We tried several combinations of gromacs versions and CUDA Toolkits. No
> > Toolkit older than 9.2
On Thu, Jan 31, 2019 at 3:18 PM wrote:
>
>
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> On Behalf Of Szilárd Páll
> Sent: Thursday, January 31, 2019 7:06 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Gromacs 2018.5 with CUDA
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Szilárd Páll
Sent: Thursday, January 31, 2019 7:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Gromacs 2018.5 with CUDA
On Wed, Jan 30, 2019 at 5:14 PM wrote:
>
> Vlad,
>
>
Run the tutorials
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Satya
Ranjan Sahoo
Sent: Wednesday, January 30, 2019 11:19 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] (no subject)
Sir,
I am a beginner to GROMACS. I was unable to understand
gmx mdrun -debug N
where N is the debug level, can be 1/2.
--
Szilárd
On Mon, Jan 28, 2019 at 3:49 PM Mahmood Naderan wrote:
>
> Hi
> Where should I set the flag in order to see the fprintf statements like
> if (debug)
> {
> fprintf(debug, "PME: number of ranks =
On Wed, Jan 30, 2019 at 5:15 PM Tafelmeier, Stefanie
wrote:
>
> Dear all,
>
> We are facing an issue with the CUDA toolkit.
> We tried several combinations of gromacs versions and CUDA Toolkits. No
> Toolkit older than 9.2 was possible to try as there are no driver for nvidia
> available for a
On Wed, Jan 30, 2019 at 5:14 PM wrote:
>
> Vlad,
>
> 390 is an 'old' driver now. Try something simple like installing CUDA 410.x
> see if that resolves the issue. if you need to update the compiler, g++ -7
> may not work, but g++ -6 does.
It is worth checking compatibility first. The GROMACS
Den 2019-01-31 kl. 12:28, skrev Özge ENGİN:
Hi All,
I am working on 3 systems in parallel: 1) protein only, 2) protein+ligand1
and 3) protein+ligand2 using the same protein. Here, I want to get rmsf
profiles of the systems along the first and second eigenvectors which can
be get by gmx anaeig
On Wed, Jan 30, 2019 at 4:56 PM Владимир Богданов
wrote:
>
> HI,
>
> Yes, I think, because it seems to be working with nam-cuda right now:
Of course, because in the meantime you upgraded your driver. NAMD, or
in fact any program that uses CUDA 9.2 will _not_ run with drivers
incompatible with
On Wed, Jan 30, 2019 at 7:37 AM Владимир Богданов <
bogdanov-vladi...@yandex.ru> wrote:
> Hey everyone!
>
> I need help, please. When I try to run MD with GPU I get the next error:
>
> Command line:
>
> gmx_mpi mdrun -deffnm md -nb auto
>
>
>
> Back Off! I just backed up md.log to ./#md
>
Hi All,
I am working on 3 systems in parallel: 1) protein only, 2) protein+ligand1
and 3) protein+ligand2 using the same protein. Here, I want to get rmsf
profiles of the systems along the first and second eigenvectors which can
be get by gmx anaeig -rmsf option. I want to use the eigenvectors
Dear Paul
Many thanks for your help.
As per your suggestion. Now I am able to perform a simulation using two
GPUs.
Earlier there are some unnecessary flags while installing. Now I have
modified installation like this:
cmake .. DGMX_THREAD_MPI=ON -DGMX_GPU=ON -DGMX_X11=ON
For running simulation
Satya,
It is helpful to have a subject in your messages. A possible start:
http://www.mdtutorials.com/gmx/index.html
Benson
On 1/31/19 7:18 AM, Satya Ranjan Sahoo wrote:
> Sir,
> I am a beginner to GROMACS. I was unable to understand how to create all
> the ions.mdp , md.mdp , mout.mdp ,
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