Re: [gmx-users] Time accounting and performance

Hi, The various kinds of balance look great, and it is entirely normal to spend all the wall time either computing forces or waiting for them to be used elsewhere. You're more than a factor of ten from the scaling limit though... Without GPUs, planning to use 500 or less atoms per x86 core has

[gmx-users] Time accounting and performance

Dear all, I use 128 ranks in 4 nodes to run GROMACS on a pretty large system containing around 85 atoms. #PBS -l select=4:ncpus=32:mpiprocs=32 -n 128 gmx_mpi mdrun -ntomp 1 -deffnm eql1 -s eql1.tpr -rdd 1.5 -dds 0. -npme 8 -ntomp_pme 1 -g eql1.log Below is the statistic of the

[gmx-users] question about the comm-mode

Hello GROMACS users, I have a quick question about the comm-mode. I want to study the protein dynamics in water. The default value of nstcomm is 100 which used to be 10. Which one is better for my case? Best, Wukai -- Gromacs Users mailing list * Please search the archive at

[gmx-users] nonbond_params directive

Hello GROMACS users, I have a quick question about the nonbond_params directive. If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive, GROMACS will (1) compute VDW parameters for all atomtype-pairs and (2) scale all 1-4 interactions specified in the pairs directive by 0.5. Note

[gmx-users] Fw: .gro file shows the wrong mass

Dear all, I tried to create Potassium-acetate .gro file using "acpype", and the same procedure works well with Sodium-acetate. The problem is when I open the .gro file in VMD for NA_ACC the mass for Sodium is correct, but for K_ACC it shows the mass of Potassium as 12 which is wrong.I

[gmx-users] .gro file shows the wrong mass

Dear all, I tried to create Potassium-acetate .gro file using "acpype", and the same procedure works well with Sodium-acetate. The problem is when I open the .gro file in VMD for NA_ACC the mass for Sodium is correct, but for K_ACC it shows the mass of Potassium as 12 which is wrong.I attached

[gmx-users] how to rename my hydrogens before pdb2gmx

Hi Gromacs users, I’d like to use pdb2gmx on a structure to which I’ve added hydrogens I’d like to keep, that is, I don’t want to use –ignh, which is the typical recommendation I see. However, I’m finding that gromac’s hydrogen nomenclature isn’t one I’m familiar with. Take PRO for example

[gmx-users] xdrfile library problem on Ubuntu 18.04 LTS

Dear GROMACS users and developers, I have problem with xdrfile library during reading *.xtc from python scripts. A month ago operating system of collectively used computer was upgraded from Ubuntu 12.04 LTS to Ubuntu 18.04 LTS. Since this, xdrfile library do not work even it was re-compiled. 

[gmx-users] xdrfile library problem on Ubuntu 18.04 LTS

Dear GROMACS users and developers, I have problem with xdrfile library during reading *.xtc from python scripts. A month ago operating system of collectively used computer was upgraded from Ubuntu 12.04 LTS to Ubuntu 18.04 LTS. Since this, xdrfile library do not work even it was re-compiled. 

[gmx-users] NVIDIA CUDA Alanine Scanning

Hi everyone, I am attempting to find a means to perform Alanine scanning mutagenesis with CUDA acceleration, but have yet to find a free/open-source option. AMBER and Schrödinger appear to be the only options available for these calculations on CUDA, and I'd like to avoid the hefty industry