[gmx-users] Using CPU with GPU

Dear gmx users,Could you suggest me a correct md launch configuration. I am using an University Cluster and would like use :  Nodes 3 (3 * 20) has 60 MPI processes. NVIDIA Tesla K20Xm: ( 2 GPUs ). Kindly suggest the optimal way to get fast md run. I tried as the following bash script but ends

Re: [gmx-users] Potential energy in Zwanzig relationship

Take a look at how the python code does EXP. The information you want is in the dhdl.xvg. Look at the documentation for this file, and read the header. Come back with specific questions about the file if the header and documentation are not enough. On Fri, Feb 10, 2017 at 6:47 AM, gozde ergin

Re: [gmx-users] No CUDA-capable device is detected

Hi Li, What does nvidia-smi return on the machine where you try to run GROMACS? Also is CUDA_VISIBLE_DEVICES set? I.e. what does echo ${CUDA_VISIBLE_DEVICES?"CUDA_VISIBLE_DEVICES is unset"} return? Even if there are GPUs in a system they could be masked out by setting

Re: [gmx-users] No CUDA-capable device is detected

Hi, The error is pretty clear about the issue: GROMACS can't detect GPUs either because there are none or because you are not able to access them (exclusive mode, you did not request them, you disabled them via CUDA_VISIABLE_DEVICES, etc.). I suggest that you contact your admin as most likely an

Re: [gmx-users] Gromacs and Radeon Nano

PS: A promising path for AMD hardware is the ROCm stack (http://gpuopen.com/compute-product/rocm/) which is the new fully open source compute driver/runtime/compiler suite. OpenCL support is very preliminary in v1.4 and I have not tried it myself yet, so I can not recommend it, but hopefully soon

[gmx-users] No CUDA-capable device is detected

Dear GMX users, I have a problem with the Gromacs jobs run on GPU node. I have the output in the log file attached below. Anyone know if the CUDA and GROMACS are compiled correctly according to this output? Is so, why does the job cannot run on GPU? Thank you very much! gmx_mpi mdrun -deffnm

[gmx-users] No CUDA-capable device is detected

Dear GMX users, I have a problem with the Gromacs jobs run on GPU node. I have the output in the log file attached below. Anyone know if the CUDA and GROMACS are compiled correctly according to this output? Is so, why does the job cannot run on GPU? Thank you very much! gmx_mpi mdrun -deffnm

Re: [gmx-users] Gromacs and Radeon Nano

Hi, I have no knowledge of the instability/crash with fglrx; with AMDGPU-PRO I have seen strange hangs which *seem* to be kernel-space issues because the machine becomes unresponsive for second to minutes (but it typically recovers). However, I had no time to investigate Given that the extensive

Re: [gmx-users] Potential energy in Zwanzig relationship

Dear Michael. Thanks for the reply. I have already used this python code however I would like to calculate myself by using the potential energies. Because I need to reweigh the free energy by using exponential re-weighting technique. > On 10 Feb 2017, at 14:44, Michael Shirts

Re: [gmx-users] Potential energy in Zwanzig relationship

https://github.com/MobleyLab/alchemical-analysis Takes gromacs dhdl.xvg output and calculate free energies by many different methods, including BAR, MBAR and Zwanzig. See http://www.alchemistry.org/wiki/Main_Page for more information. On Fri, Feb 10, 2017 at 5:26 AM, gozde ergin

Re: [gmx-users] Plumed with GROMACS 5.1.2

Hi Amit, You patch plumed onto the gromacs source and then yes you need to recompile gromacs. It may help to look at this thread from the plumed google group https://groups.google.com/forum/#!topic/plumed-users/stlK9-kaa6A where I worked out how to do it. I was using plumed 2.1 which had some

[gmx-users] Potential energy in Zwanzig relationship

Dear all, I run thermodynamic integration simulation with gromacs and got the free energy by g_bar command. I also would like to estimate this free energy by using Zwanzig relationship of \DeltaG = -RT ln (_i Here U is the potential energy, right? However the results

Re: [gmx-users] run parameters

Dear Nikhil, It depends, but generally no electrostatic cut-offs since there is no dielectric medium, making the effective range of electrostatics very long. And no pbc. If you are doing NVE with constraints you might want to increase lincs-iter and -order from their default values. Kind

[gmx-users] run parameters

hii What will be the best mdp file options for production run for polymer in vacuum simulation.? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] g_wham PMF Profiles

Hi, I appreciate your answer. Simulation time is 200 ns per window. Our pulling rate for the initial pulling simulation is 0.01, but the interval between subsequent umbrella windows are 0.1 nm. When I try to add additional windows to the region around 1.3 nm they drift away from that position;

[gmx-users] NVT error

VNT error: 5.0.7 ff 43A1 error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values read from gromacs mail list "Precisely what it says. You specify one group to be coupled (System), but then provide coupling information for two groups." i have no idea to correct my own NVT

[gmx-users] Plumed with GROMACS 5.1.2

Hello, I have installed plumed 2.3. But I am having doubt in the patching process. Where should I patch the executable? Do I need to recompile gromacs after patching ? Thanks Amit Behera -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be

Re: [gmx-users] g_wham PMF Profiles

Hi Zeynep, As you exclude the window, you lost the local information. But even excluded PMF profile does not seem that ’smooth’. What is your simulation time? And maybe you may think of pulling slower like 0.01 nm spacing. bests (iyi calismalar) > On 10 Feb 2017, at 08:57, ZEYNEP ABALI