Re: [gmx-users] Compatibility of gromacs 2018.3 with Cuda 10

> On 14. Feb 2019, at 08:19, Sujit Sarkar wrote: > > Dear gmx-users, > Is Gromacs 2018.3 installation supported by Cuda 10.0 toolkit? Yes. Carsten > Thanks, > Sujit > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Use

[gmx-users] Compatibility of gromacs 2018.3 with Cuda 10

Dear gmx-users, Is Gromacs 2018.3 installation supported by Cuda 10.0 toolkit? Thanks, Sujit -- 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 http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Automatic calculation of several RDFs

Dear all I want to obtain the change of RDFs for 1ns interval during simulation. My simulation time is 200 ns. Since my simulation box is large, it's time consuming. Is it possible to define a script to calculate RDFs one after another? Let me rephrase my question. Can I select the groups, which

Re: [gmx-users] Performance of GROMACS on GPU's on ORNL Titan?

For what it is worth: on our AMD 2990wd 32 core, 2 x 2080ti we can run 100k atoms at ~ 100ns/day NVT , ~ 150 ns/day NPT so 8 -10 days to get that microsecond. I'm curious to learn what kind of results you might obtain from Oak Ridge and if the cost/clock time analysis makes it worthwhile. Paul

[gmx-users] Performance of GROMACS on GPU's on ORNL Titan?

Does anyone have experience running GROMACS on GPU's on Oak Ridge National Labs Titan or Summit machines, especially parallelization over multiple GPUs? I'm looking at applying for allocations there, and am interested in experiences that people have had. We're probably mostly looking at systems in

[gmx-users] Can I take any conformational sub state from REMD

Dear gromacs users I have 20 residues length of peptide and it has some helix content. I have done REMD (with lower temperature range 300K and upper temperature 450K) to denature the helix. I gave desired exchange probability 0.25 and I got 30 temperature points and I did REMD simulations all 30

Re: [gmx-users] Fwd: Maximum number density in gmx densmap

Dear all, Any idea on my questions, please? Mostafa; Using gmx densmap first produce a .xpm file; ~> gmx densmap -f case.xtc -s case.tpr -n index.ndx -o case.xpm -unit nm-3 -bin 0.02 The case.xpm file is a matrix, one way provided by Gromacs to visualize a matrix is to convert it to a eps file for