Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. On Mon, Mar 24, 2008 at 3:08 PM, maria goranovic [EMAIL PROTECTED] wrote: Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem. No particular

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

maria goranovic wrote: An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. As you can see in some of the original PME papers, tweaking the parameters can give about an order of magnitude variation in the approximation error for given

[gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 16 atoms) using the same gromacs installation

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

Am 24.03.2008 um 10:17 schrieb maria goranovic: Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

The end of the log files after the simulation finishes might help you understand if there's anything odd that's taking more computation than normal. Also, just one extra running process can slow down the entire simulation as all processors will wait for the slowest. Check if it takes as long if

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem. No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway. thanks ! -maria On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner [EMAIL PROTECTED]