Hi Paul,
I just jumped in this discussion. But I am wondering is
CUDA_VISIBLE_DEVICES equivalent to providing gpu_id in mdrun?
Also, my multiple simulations run slower in the same node with multiple
gpus. e.g. in a node with 4 GPU and 64 CPU
mpirun -np 1 mdrun -ntomp 24 -gpu_id 0 -pin on
mpirun
Hello,
the error you are getting in the end means that your simulation likely
does not use PME, or uses it in a way that is not implemented to run on
the GPU.
You can still run the nonbonded calculations on the GPU, just remove the
-pme gpu flag.
For running different simulations on your
Dear Gromacs users,
I am simulating a protein-ligand complex and performing the grompp command
before adding ions to the system. I got the error.
*Fatal error: *(file: ligand.itp)
Atomtype *CH2 not found*.
*command used:*
gmx grompp -f ions.mdp -c protein_box.gro -p protein.top -o ions.tpr
Please
Thanks Nikhil.
About the second question. It is actually implemented , as you can see the
link below, however I cannot run these commands without error.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-July/126012.html
On Fri, Dec 13, 2019 at 12:28 PM Nikhil Maroli wrote:
>
You can assign part of the core and 1 GPU to one job and another part with
separate command.
For ex.
1. gmx mdrun -ntmpi XX -ntomp YY -gpu_id K1
2. gmx mdrun -ntmpi XX2 -ntomp YY2 -gpu_id K2
the second part of the question is related to the implementation of such
calculations in GPU< which is
You could do that (maintain the "center" of the droplet in the frame) is to
remove those molecules that exit and return to the droplet, and then use
the remaining molecules as the index group to determine the COM to which
things are then centered on.
Catch ya,
Dr. Dallas Warren
Drug Delivery,
Hello all,
I am running a polymer melt with 10 atoms, 2 fs time step, PME, on a
workstation with specifications:
2X Intel Xeon 6128 3.4 2666 MHz 6-core CPU
2X16B DDR4 RAM
2XRTX 2080Ti 11 GB
I have installed *GPU and thread_mpi *enabled gromacs 2019.0 version using:
cmake ..
Dear Justin,
As you recommended I invoked the trjconv -pbc cluster and trjconv -center
separatedly, and also, I used a proper reference .gro file (where
everything is intact) in tpr file.
Here are the command I invoked in order on my trajectory:
1. gmx trjconv -f orig.xtc -o mol.xtc -pbc mol ...
Hi,
On Thu., 12 Dec. 2019, 20:27 Marcin Mielniczuk,
wrote:
> Hi,
>
> I'm running Gromacs on a heterogenous cluster, with one node
> significantly faster than the other. Therefore, I'd like to achieve the
> following setup:
> * run 2 or 3 PP processes and 1 PME process on the faster node (with a
Get more memory or process a smaller amount (atoms or trajectory).
http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#out-of-memory-when-allocating
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences,
Hi Christian,
I see, ok. Thanks a lot for your feedback, really helpful!
Best,
Ramon
On Thu, Dec 12, 2019 at 1:22 PM Christian Blau wrote:
> Hi Ramon,
>
>
> You would not need to keep your system constrained in the state that you
> started from to see a transition. Pushing state
> A , based
Hi,
I'm running Gromacs on a heterogenous cluster, with one node
significantly faster than the other. Therefore, I'd like to achieve the
following setup:
* run 2 or 3 PP processes and 1 PME process on the faster node (with a
lower number of OpenMP threads)
* run 2 PP processes on the slower node
Hi!
I've just realized that my reply stayed in drafts.
This worked for me, thanks a lot!
Btw. if anyone else encounters such a problem: tune_pme works out of the
box only if a shared filesystem is present. Otherwise, the modified tpr
files need to be copied manually between the nodes.
Regards,
Hi gromacs users
I want to restraint distance, angles and dihedrals between atoms of two
different residues; In my case protein atom and ligand atom. Could anybody
suggest me the right way of doing it?
I have set topology file of complex as below:-
Include forcefield parameters
#include
Hi Mark
Multiple energy groups is not implemented for GPUs, falling back to the
CPU. For better performance, run on the GPU without energy groups and then
do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
I got this line on the log file.
gmx_mpi mdrun -v -deffnm md
Hi,
On Thu, 12 Dec 2019 at 15:03, Paul Buscemi wrote:
> What does nvidia-smi tell you?
>
That won't inform - GROMACS isn't saying it can't find GPUs. It's saying it
can't run on them because something Rahul asked for isn't implemented.
Mark
PB
>
> > On Dec 12, 2019, at 7:30 AM, John
What does nvidia-smi tell you?
PB
> On Dec 12, 2019, at 7:30 AM, John Whittaker
> wrote:
>
> Hi,
>
>> Hi Users.
>>
>> I am simulating a peptide of 40 residues with small molecules using oplsaa
>> ff in Gromacs 2018.20 installed in CUDA environment.. The workstation has
>> 16 Cores and 2
Hi,
On Thu, 12 Dec 2019 at 14:35, Mateusz Bieniek wrote:
> Hi Gromacs,
>
> A small digression: Ideally Gromacs would make it more clear in the error
> message explaining which part is not implemented for the GPUs.
>
Indeed, and this case it is supposed to have already written on the log
file
Hi,
I suspect that you have multiple versions of hwloc on your system, and
somehow the environment is different at cmake time and make time (e.g.
different modules loaded?). If so, don't do that. Otherwise, cmake
-DGMX_HWLOC=off will work well enough. I've proposed a probably fix for
future 2019
Hi Gromacs,
A small digression: Ideally Gromacs would make it more clear in the error
message explaining which part is not implemented for the GPUs.
Thanks, Mat
On Thu, 12 Dec 2019 at 13:01, RAHUL SURESH wrote:
> Hi John
>
> Thank you and adding here the mdp settings
>
> title =
Hi John
Thank you and adding here the mdp settings
title = Protein-gas molecule interaction MD simulation
; Run parameters
integrator = md
nsteps = 2
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000;
nstvout = 5000 ;
nstenergy = 5000;
Hi,
> Hi Users.
>
> I am simulating a peptide of 40 residues with small molecules using oplsaa
> ff in Gromacs 2018.20 installed in CUDA environment.. The workstation has
> 16 Cores and 2 1080Ti card On execution of command gmx_mpi mdrun -v
> -deffnm
> md for 100ns it shows no usage of gpu card.
Hi Users.
I am simulating a peptide of 40 residues with small molecules using oplsaa
ff in Gromacs 2018.20 installed in CUDA environment.. The workstation has
16 Cores and 2 1080Ti card On execution of command gmx_mpi mdrun -v -deffnm
md for 100ns it shows no usage of gpu card. For the command
Hi Ramon,
You would not need to keep your system constrained in the state that you started from to see a transition. Pushing state
A , based on a crystal structure, into state B , described by a density, should give you just the transition you want.
If you would like to choose an arbitrary
hi,
i want to calculate the tilt angle of helix against the bilayer normal.
First i made a index file which contains the backbone of the residues of
large helix. I am using this command
*gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise
-oradius -otwist -obending -otilt -orot*
Hello,
I'm trying to install gromacs-2019.4 with GPU support, but was always wrong.
I ran cmake as
cmake3 .. -DCMAKE_INSTALL_PREFIX=~/gromacs/gmx2019.4 -DGMX_BUILD_OWN_FFTW=ON
-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_HWLOC=ON
It works but when installing always get error
Hi Christian,
Ok, so If can't apply forces from two density maps at the same time then I
don't see how can I perform a guided transition.
I mean, I figured I would need to gradually switch on one map while
switching off the other, but for this I need to apply both restraints at
the same time
Hi Ramon,
This feature will be released in January ;) and is in a beta version, soon to be release candidate, so you are
definitely an early adopter.
Most of the parameters are set by default in the .mdp file if you do not set
them yourself, you'll see them also in
On 12/12/19 12:49 AM, atb files wrote:
Hello Experts,What is the use of -nice option in gmx mdrun? What it does? When to use it? What are it’s benefits?-YogeshSent using Zoho Mail
https://en.wikipedia.org/wiki/Nice_(Unix)
-Justin
--
Hi Christian,
thanks a lot for your answer. Good to know this makes sense to someone else
too.
Now I have two questions out of ignorance (never used this newly
implemented feature before):
1) Can I apply two sets of forces (restraints) at the same time, namely one
for each density map?
2) Would
Hi Paul,
Thanks. My replies below:
On Thu, Dec 12, 2019 at 2:32 AM Paul bauer wrote:
> Hello,
>
> I'll have a look later today.
> Can you also give as information about your build configuration?
>
If I am not wrong you mean this:
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
Hello,
I'll have a look later today.
Can you also give as information about your build configuration?
If you could upload a log file from mdrun to Redmine it should be enough.
Thanks
Paul
On 12/12/2019 11:28, Dave M wrote:
Hi Mark,
Thanks just opened new issue. My all simulations are
Hi Ramon,
This is definitely a way to obtain a transition path.
One things to consider here is that you deliberately "throw away" already perfect information about your target
structure, so it might be harder to reach. On the other hand you might not care to have an exact overlap with the
Hi Mark,
Thanks just opened new issue. My all simulations are performed using
gromacs2019.4 and to be consistent to report the results I would like to
keep same version. But this specific case is creating trouble. What is best
I can do? if I use a different gromacs version for this specific case
Dear All,
I'm coming across the error "Failed to calloc -9223372036854775808 elements
of size 8 for bin" while running gmx spatial.
I have three four systems and for the others -nab option with 100 worked
fine but here, even after increasing -nab to 1000 , it shows insufficient
memory.
What could
Hi,
That sounds very much like a bug, but it's hard to say where it comes from.
Can you please open an issue at https://redmine.gromacs.org/ and attach
your .tpr files plus a log file from a failing run and the above stack
trace?
Mark
On Thu, 12 Dec 2019 at 08:37, Dave M wrote:
> Hi All,
>
>
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