[gmx-users] Running all the processors in HPC

Hi, I am trying to run a 'Protein-Ligand' complex in our university's HPC. There are 32 processors in the cluster. But, while running mdrun it runs in only one CPU. How to cluster all the processors in the HPC? I have searched internet with no luck. The version is 4.6. I also tried running logged

[gmx-users] Mn/Mn2+ Parameters included in Amberff

Hello It looks like parameters for Mn/Mn2+ were (somewhat) recently developed for Amber forcefield (http://pubs.acs.org/doi/abs/10.1021/ct400055v); I'd like to use these parameters for a simulation I'd like to run on MntR (PDB: 1ON2 ), but

Re: [gmx-users] pressure and density

On Sun, Jun 26, 2016 at 12:04 PM, Mark Abraham wrote: Hello Mark and thank you for your response. > Hi, > > On Sat, Jun 25, 2016 at 5:27 PM Alexander Alexander < > alexanderwie...@gmail.com> wrote: > > > Dear gromacs user, > > > > I have a system containing a solid

Re: [gmx-users] Segmentation Fault - Water on Substrate

Hi Mark, Thanks for your quick response. In the all three minimisation.mdp files (the one for water.pdb, substrate.pdb and merged.pdb) I have: pbc = xyz To minimise the water.pdb file I have: periodic_molecules = no ; To minimise the substrate.pdb and then the merged.pdb

Re: [gmx-users] pressure and density

Hi, On Sat, Jun 25, 2016 at 5:27 PM Alexander Alexander < alexanderwie...@gmail.com> wrote: > Dear gromacs user, > > I have a system containing a solid surface(18000 atoms) and on top of it a > heptapeptide solvated in water(SOL 9604), after a good minimisation and > NVT equilibration and

Re: [gmx-users] Segmentation Fault - Water on Substrate

Hi, You're presumably making one of your formerly periodic dimensions differently periodic when you combine your boxes. If your input structure has molecules with coordinates that are broken across the former boundary, you need to make them whole before your merge can work sanely. Mark On Sun,

[gmx-users] Segmentation Fault - Water on Substrate

Dear Gromacs users, I am want to simulate water on a substrate. I have a water.pdb file with the coordinates of a cuboid of water and a substrate.pdb file with the coordinates of the substrate. The box dimensions along the x and y directions are identical for both files. I run two simulations

Re: [gmx-users] wrap only in XZ?

Sorry made a mistake in typing. I only would like to wrap in XY, not XZ. Leaving the Z unwrap. Rotate the system along which axis for 90 degree? I see some people use "wall" + PBC in XY only. However, it needs to define "wall_atomtype", I don't know how to define this THX On

Re: [gmx-users] wrap only in XZ?

Hi Albert, Rotate the system 90 degrees and use PBC in xy only. Cheers, Tsjerk On Jun 26, 2016 9:04 AM, "Albert" wrote: > Hello: > > I've got a membrane protein system and I would like the water and ions > only wrap in XZ direction. Currently, they can also wrap at Z

[gmx-users] wrap only in XZ?

Hello: I've got a membrane protein system and I would like the water and ions only wrap in XZ direction. Currently, they can also wrap at Z direction. I am just wondering how can we prevent them wrap at Z direction? Thank you very much. Albert -- Gromacs Users mailing list * Please search