Thanks for the heads up. With the K40c instead of GTX 960 here's what I
did and here are the results:
1. Enabled persistence mode and overclocked the card via nvidia-smi:
http://acceleware.com/blog/gpu-boost-nvidias-tesla-k40-gpus
2. Offloaded PME's FFT to GPU (which wasn't the case with GTX
Thank you Shreyas, Pedro and Mark Abraham for forwarding my initial message to
the program's author who responded to me
Stéphane
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Message: 3
Date: Sat, 16 Jun 2018 19:45:28 +0200
From: Shreyas Kaptan
Hi.
Maybe you already know this but you can also build the whole embedded
system with charmm-gui. Also, your parameters appear reasonable to me at
first glance.
As for the equilibration, that is a system specific question. If you have a
"simple" uniform lipid content in the bilayer I would say
Dear Gromacs users,
I'm new in the field of Molecular Dynamics especially in using Gromacs.
I have several questions regarding mdp file and I'll be very grateful if
you can help me with them.
I'm using a membrane-protein system with Charmm36 ff. After I have
constructed bilayer membrane by using
