Re: [gmx-users] Gomacs and multiple GPU

Hi, thank you for your answer the Cmdline is: gmx mdrun -deffnm nvt I played a bit with option -gpu_id, use $CUDA_VISIBLE_DEVICES and read the page http://www.gromacs.org/GPU_acceleration without any succes. One output is in nvt.log.11, nvidia-smi returs is in nvidia-smi.log Nvidia-smi

Re: [gmx-users] Gomacs and multiple GPU

Alexis, What is the problem? Have you read the relevant docs of what CUDA_VISIBLE_DEVICES does? https://docs.nvidia.com/cuda/cuda-c-programming-guide/#env-vars BTW, you can use, but you *do not need* CUDA_VISIBLE devices to control the mapping of GPU(s) to mdrun process, the -gpu_id variable

Re: [gmx-users] Neighbor searching artifacts in permittivity when using shift

Hi, Unless you are actually not using the Verlet scheme (or you have set the tolerance to -1), rlist has no effect, it is not used in any way as it is calculated automatically for the given system and settings. Hence, your observation that > The permittivity was even stronger influenced by

Re: [gmx-users] Gomacs and multiple GPU

Hi, Do any other programs, e.g. CUDA SDK samples (like deviceQuery) detect both GPUs? I find it *very-very* unlikely that only mdrun would not be able detect both GPUs. Again, are you sure it's not the use of CUDA_VISIBLE_DEVICES that creates the confusion? Please share your full command line

Re: [gmx-users] Lattice distance for HII phase

Dear gromacs users, I appreciate your opinion on this email in advance. Cheers Mohsen On Thu, Nov 17, 2016 at 11:07 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear Gromacs users, > > I have a HII phase made of molecules. HII phase is formed of many > cylinders parallel to

Re: [gmx-users] Gomacs and multiple GPU

Hi, Welcome! > Thank for you reply. Yes, i have read them and know them. I use them will success with other software. BTW, what did you refer to here? It seems like you were focused on figuring out the detection issue and might have ignored my other recommendations on using multi (which

[gmx-users] Computer processor and graphics card choice

Dear colleagues, I want to buy a computer to perform molecular dynamics by GROMACS, and I have several questions. First of all, I am having doubts between the Intel Xeon E5-2620v4 (8 cores, 2.1-3.0 GHz) and the i7-5820K (6 cores, 3.3-3.6 GHz). The reason of my doubts is the significantly

[gmx-users] order parameters for Inverted hexagonal phase

Dear Gromacs Users, I have a question on how to use g_order to get the order parameters correctly for an inverted hexagonal (HII) phase and compare it with experimental values from NMR. I read some articles, including following one: Vermeer, Louic S., et al. "Acyl chain order parameter profiles

Re: [gmx-users] Computer processor and graphics card choice

Hi Guillem, I can answer your last question - the 10xx series does indeed work well with GROMACS (currently running GROMACS 2016 with a GTX1070), although I would be inclined to get the GTX1070 if your budget can stretch to it. Andrew On Fri, Dec 2, 2016 at 6:15 AM, Guillem Prats Ejarque <

Re: [gmx-users] hbond

On 12/1/2016 7:45 AM, Justin Lemkul wrote: On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote: Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water

Re: [gmx-users] Gomacs and multiple GPU

Hi, Thank for you reply. Yes, i have read them and know them. I use them will success with other software. My first and main problem is mdrun doesn't see the second GPU on the system. And i try to find the root cause of and the remediation. Hardware is a bi xeon with 2 Titan-xp GPU, so my goal

Re: [gmx-users] Gomacs and multiple GPU

Hi, You solve my problem, Thank you. The variable CUDA_VISIBLE_DEVICES is set up by the scheduler at the running time of my job. So after adding commandline "unset $CUDA_VISIBLE_DEVICES" in my script, mdrun detect and use both GPUs. Thank you for your patience. Cheers, Alexis On 01/12/16

[gmx-users] system blowing up

Hi, I'm constantly getting a strange error of system blow up during equilibration procedure. I'm relatively new to gromacs, please help me to get my things straight. I have a ligand bound protein structure in solvated condition. So, I was using: gmx mdrun -v -deffnm em #for minimization Upon

Re: [gmx-users] Problem in PMF simulation

Thanks :) On 1 December 2016 at 23:40, Justin Lemkul wrote: > > > On 12/1/16 4:53 AM, Billy Williams-Noonan wrote: > >> Also, you may want to check that your rcoulomb and rvdw values are >> correct... Didn't look at your mdp files until just now. Why are they >> set >> to

[gmx-users] COM group of Membrane and Protein simulation

Dear gmx_users, I started simulation that a peptide on membrane. My peptide locates on the membrane surface. I have two questions relating to the simulation. (1) When I start the simulation, I chose COM groups separately. Is this choice okay? or May I need to chose COM group inseparately? (2)

[gmx-users] parallel processing

Hi, I'm running gromacs on a cluster configuration as follows: 1 node = 16 cores I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v -deffnm em" command. How can I be able to run on multiple node (I have 20 nodes available) ? "-nt" is not doing good here. -- Abhisek

[gmx-users] Desired spacing in umbrella sampling

Dear Gromacs users, Is it reasonable to choose asymmetric windows in umbrella sampling? I want to use 0.1 nm spacing for 0.6-2.6 COM distance and then 0.2 nm for 2.6-5.3. Regards, Farideh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water insertion". There is nothing in the online documentation as to how this should be done except a

Re: [gmx-users] Problem in PMF simulation

On 12/1/16 4:53 AM, Billy Williams-Noonan wrote: Also, you may want to check that your rcoulomb and rvdw values are correct... Didn't look at your mdp files until just now. Why are they set to zero? Vacuum simulations are done with infinite cutoffs (rlist=rcoulomb=rvdw=0) and no PBC.

Re: [gmx-users] Problem in PMF simulation

Also, you may want to check that your rcoulomb and rvdw values are correct... Didn't look at your mdp files until just now. Why are they set to zero? On 29 November 2016 at 16:56, Billy Williams-Noonan < billy.williams-noo...@monash.edu> wrote: > My PMF curves look similar to that. What

[gmx-users] bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary file

Dear gromacs users, export SOFT=$HOME/installation export CPPFLAGS="-I$SOFT/include" export LDFLAGS="-L$SOFT/lib" export PATH="$PATH":$SOFT/bin tar xvf cmake-3.6.1.tar.gz cd ../cmake-3.6.1. ./configure --prefix=$SOFT make make install tar xvzf gromacs-5.1.3.tar.gz cd ../gromacs-5.1.3 mkdir

Re: [gmx-users] Gomacs and multiple GPU

Hi, On Wed, Nov 30, 2016 at 5:38 PM Alexis Michon wrote: > Hello, > > We have build gromacs 2016.1 from source with "DMX_GPU=on" on a bi > processor bi GPU machine, mdrun detect and run fine on only 1 GPU. How > could we force mdrun to detect the second GPU ? > If it's

Re: [gmx-users] bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary file

Hi, That shouldn't happen. Are you able to install and run other software similarly? I note that your gmx_mpi binary is quite old, and your cmake command misspelled -DCMAKE_INSTALL_PRIFFIX=$SOFT so perhaps you are simply not doing what you think/say you are doing. Mark On Thu, Dec 1, 2016 at

Re: [gmx-users] gmx insert-molecules not adding the required number of molecules

Hi, Adding a big thing, then lots of small things randomly and then lots of medium sized things randomly isn't going to work very well to give you something approximately close-packed at the end. You're just not likely to end up with exactly enough holes suitable for things of medium size. So

Re: [gmx-users] PME

Hi, Not directly, and anyway the PME grid only has the long-ranged component of anything. You could use mdrun -rerun to compute the potential via adding a new test particle to the system in its own energy group and observing its energy as you move its position. Mark On Wed, Nov 30, 2016 at 7:11

Re: [gmx-users] Order Parameter with an all-atom force field

On 11/29/16 7:50 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, I have a question on S_cd order parameters: Using g_order for a lipid like DSPC, I can get the values for C2 to C17, although DS tail has 18 carbons. I know the reason when I use a united atom force field like Gromos54A7.

Re: [gmx-users] (no subject)

On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote: Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water insertion". There is nothing in the online