[gmx-users] increasing md run speed

neelam wafa neelam.wafa at gmail.com
Sat Jun 23 04:56:21 CEST 2018

Dear gmx users!

I am running md simmulation of a protein with different ligands but the
speed is decreasing with every simmulation. In first one it was 25hrs/ns,
for second one it became 35 hrs/ns then 36hs/ns. what can be the reason?
I am using this command for the run.
How to select the value of x if I use this command to increase the speed.
Following is the detail of the cores used and the hardware i am using.

Running on 1 node with total 2 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Core(TM) i3-2370M CPU @ 2.40GHz
    SIMD instructions most likely to fit this hardware: AVX_256
    SIMD instructions selected at GROMACS compile time: AVX_256

Reading file em.tpr, VERSION 5.1.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads

Looking forward for your help and cooperation.

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