---------- Forwarded message ----------
From: Chhaya Singh <chhayasingh014.gmail.com>
Date: 24 June 2018 at 12:47
Subject: increase speed in amber using implcit solvent model
To: amber.ambermd.org
Hi,
I am trying to perform a simulation having a protein using implicit solvent
model using force field ff14sbonlysc with igb = 8.
I am getting a very low speed using 2 nodes. the speed i get now is less a
ns/ day.
is there a way to increase speed in amber.
please let me know.
my min.in file has :
Stage 1 - minimisation of fibril
&cntrl
imin=1, maxcyc=1000, ncyc=500,
cut=999., rgbmax=999.,igb=8, ntb=0,
ntpr=100
/
my heat1.out file has:
Final Performance Info:
| -----------------------------------------------------
| Average timings for last 50 steps:
| Elapsed(s) = 17.41 Per Step(ms) = 348.14
| ns/day = 0.12 seconds/ns = 696286.68
|
| Average timings for all steps:
| Elapsed(s) = 3487.17 Per Step(ms) = 348.72
| ns/day = 0.12 seconds/ns = 697434.94
| -----------------------------------------------------
| Master Setup CPU time: 0.26 seconds
| Master NonSetup CPU time: 3461.87 seconds
| Master Total CPU time: 3462.13 seconds 0.96 hours
| Master Setup wall time: 1 seconds
| Master NonSetup wall time: 3487 seconds
| Master Total wall time: 3488 seconds 0.97 hours
can you please help. how can I increase the speed using implicit solvent in
amber.
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Received on Sun Jun 24 2018 - 00:30:03 PDT
