Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

Hi, Intel GPUs require cluster size 4. AMD GPUs perform best with 8. Does GROMACS recognize both GPUs (should be in the log file) if you compile with cluster size 4? If so you should be able to select which GPU it uses with the -gpuid command line argument. But I have never tried it with

Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

Hi Roland, Thank you for the reply. The file (nbnxn_ocl_kernel_pruneonly.clh) does exist in that folder, so I’m not sure why it isn’t being located. I’ve downloaded the latest versions of Gromacs, and I will try building them as soon as I can. Is there any reason to specify

Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

Hi, Does the nbnxn_ocl_kernel_pruneonly.clh file exist in the /Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl folder? When reporting errors you should always check with the latest version. The latest versions are 2019.1 and 2018.5. Roland > -Original Message- >

[gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

Hi, I’ve been trying to build Gromacs 2018.3 on my MacBook Pro (in OSX 10.14.3). I saw online (https://redmine.gromacs.org/issues/2369 ) that Gromacs with GPU support via OpenCL was found to work a similar computer, but I have not had any luck. Is there

[gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

My coarse-grained system has 10 proteins, each has 442 residues. After a period of time, those proteins aggregated. I want to use "gmx distance" to know which residues most likely to involve contact with other proteins. I prepared a index.ndx file, in which there are 442*442*(9+8+7 ... + 1) =

[gmx-users] How to replacing molecule outside the 2.5nm cutoff distance from protein surface in gromacs?

Dear gromacs users, I have protein-membrane (POPC only) system. I want to replace the cholesterol molecules with POPC but outside a 2.5nm cutoff distance of protein surface. I am using this command : gmx insert-molecules -f system.gro -ci cholesterol.pdb -nmol 10 -try 10 -replace POPC -o

[gmx-users] Making Polyamide membrane itp file

Dear gromacs users, These days, I am working on Polyamide membrane osmosis. And I am struggling with making a topology file. I've read a paper " *DOI: * 10.1021/acs.jpcb.6b06560 " . The author provides pdb file for the constructed membrane in supporting information section on the webpage. But to

[gmx-users] Computational performance in version 2019-beta3.

Hello guys, I performed a 100 ns simulation using GROMACS: gmx mdrun, version 2019-beta3. The performance of my computer was 4ns / day. In previous versions, I performed similar simulations and obtained performace of 40 ns / day. I would like to know if something has changed in gmx mdrun's input

[gmx-users] Building Gromacs on a MacBook Pro with AMD Radeon Pro 560

Hello, I’ve been having trouble building Gromacs 2018.3 on my MacBook Pro. I would like to be able to use OpenMP as well as the GPU (via OpenCL). I’ve searched for successful builds with similar systems described on this email list, but haven’t found anything that worked yet. Based on what

Re: [gmx-users] Error while running grompp command

Please send the entire error message On Sun 17 Feb, 2019, 8:16 PM Nath, Dinesh Hello, > > I am running the gmx grompp -f ions.mdp -c solv.gro -p topol.top -o > ions.tpr > > And this is the error I am getting: > > ERROR 1 [file rew.prm, line 36]: > Encountered a second block of parameters for