Re: [gmx-users] Gmx gangle (Shi Li)

> > > > Hi, > > > > I would check the documentation of gmx gangle for how it works, > > particularly for how to define a plane. > > Thank you so much Mark. As a GROMACS lover, I like to make a suggestion; I > think sth it would be REALLY helpful if you provide some proper examples > for gromacs

Re: [gmx-users] using dual CPU's

Dear users ( one more try ) I am trying to use 2 GPU cards to improve modeling speed. The computer described in the log files is used to iron out models and am using to learn how to use two GPU cards before purchasing two new RTX 2080 ti's. The CPU is a 8 core 16 thread AMD and the GPU's

Re: [gmx-users] using dual CPU's

Hi Paul, > On 12. Dec 2018, at 15:36, pbusc...@q.com wrote: > > Dear users ( one more try ) > > I am trying to use 2 GPU cards to improve modeling speed. The computer > described in the log files is used to iron out models and am using to learn > how to use two GPU cards before purchasing

[gmx-users] Getting more detail than is in the documentation

Hi! There are frequently times when I would like a lot more detail on how a command works than is in the docs. For example, with respect to the "traj" command option "-ekr", this is all it says: "Options -ekt and -ekr plot the translational and rotational kinetic energy of each group..." But,

Re: [gmx-users] gromacs 2018 with OpenMPI + OpenMP

On Wed, Dec 12, 2018 at 12:14 PM Deepak Porwal wrote: > > Hi > I build gromacs with OpenMPI + OpenMP. > When I am trying to run adh/adh_dodec workload with binding the MPI threads > to core/l3cache, I am seeing some warnings. > Command I used to run: mpirun --map-by ppr:1:l3cache:pe=2 -x >

Re: [gmx-users] Area compressibility modulus GMX

John Ain’t nothin’ silly about analyzing membranes. It’s an artform . Have you taken a look at Membplugin https://sourceforge.net/p/membplugin/wiki/Home/ it provides trajectory values for among other things thickness and area/lipid.

Re: [gmx-users] Getting more detail than is in the documentation

James, Good resource to check is the manual. I'm pretty sure most of the calculations performed / formulas used are in there somewhere? Another option is in the header text for the script itself, when appropriate there will be a reference to a paper where the code/formula/method has come from.

Re: [gmx-users] using dual CPU's

Carsten,THanks for the response. my mistake - it was the GTX 980 from fig 3. … I was recalling from memory….. I assume that similar results would be achieved with the 1060’s No I did not reset , my results were a compilation of 4-5 runs each under slightly different conditions on two

Re: [gmx-users] Getting more detail than is in the documentation

Hi Dr. Warren, Thanks for the suggestions! I did not realize that the pages which describe the commands, such as: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-traj.html are not just copies of what is in the PDF manual. The manual has more theory, formulas, and references (which

[gmx-users] gromacs 2018 with OpenMPI + OpenMP

Hi I build gromacs with OpenMPI + OpenMP. When I am trying to run adh/adh_dodec workload with binding the MPI threads to core/l3cache, I am seeing some warnings. Command I used to run: mpirun --map-by ppr:1:l3cache:pe=2 -x OMP_NUM_THREADS=4 -x OMP_PROC_BIND=TRUE -x OMP_PLACES=cores gmx_mpi mdrun

[gmx-users] Pressure annealing?

Dear Gromacs users, During NpT runs, is it possbile to increase/ decrease in a controlled way the box vectors (user-defined, the same as in temperature annealing)? Kind regards *Javier Luque Di Salvo* -- Gromacs Users mailing list * Please search the archive at