Hi,
I have a system of 1310 atoms. I have completed its simulation using the
implicit solvent model with force field ff14SBonlysc and igb = 8 with your
help. thanks for that.
now I want to perform REMD with this system.
I have tried it using the AMBER tutorial:
*AMBER ADVANCED TUTORIALS; **TUTORIAL A7*
Replica Exchange Simulations with AMBER 1*0*
*the CPU that I am using has the following details: Intel E5-2670 series
CPUs with 16 cores/node and has 64 GB RAM. The nodes are interconnected by
4X QDR InfiniBand network. I have run REMD using 8 nodes, 16cpus, and 16
processors. I am getting a speed of 18ns/ day.is there a way to increase
the speed? my output files details are as
follows:remd.mdout.001-----------------------------------------------------|
Average timings for all steps:| Elapsed(s) = 4645.03 Per Step(ms)
= 9.29| ns/day = 18.60 seconds/ns = 4645.03|
-----------------------------------------------------| Job began
at 03:12:27.958 on 07/06/2018| Setup done at 03:12:28.232 on
07/06/2018| Run done at 04:29:53.475 on 07/06/2018|
wallclock() was called17529086 times*
all the input files are taken from the tutorial itself to carry out the
REMD.
*remd.mdinfo.001 : *
* NSTEP = 500000 TIME(PS) = 1000.000 TEMP(K) = 271.52 PRESS
= 0.0 Etot = -52.9917 EKtot = 880.5565 EPtot
= -933.5482 BOND = 229.3837 ANGLE = 607.0232
DIHED = 991.5442 1-4 NB = 269.4033 1-4 EEL =
5006.0700 VDWAALS = -437.0668 EELEC = -6531.7074 EGB
= -1694.8088 RESTRAINT = 626.6105 TEMP0 = 269.5000
REPNUM = 1 EXCHANGE# = 1000 EAMBER
(non-restraint) = -1560.1586 NMR restraints: Bond = 0.000 Angle
= 0.000 Torsion =
626.610===============================================================================|
Final Performance Info:|
-----------------------------------------------------| Average timings for
last 100 steps:| Elapsed(s) = 0.97 Per Step(ms) =
9.66| ns/day = 17.89 seconds/ns = 4829.83|| Average
timings for all steps:| Elapsed(s) = 4644.98 Per Step(ms) =
9.29| ns/day = 18.60 seconds/ns = 4644.98|
-----------------------------------------------------*
*remd.mdin.001 :*
*libration &cntrl irest=0, ntx=1, nstlim=500, dt=0.002, irest=0,
ntt=3, gamma_ln=1.0, temp0=269.5, ig=13788, ntc=2, ntf=2, nscm=1000,
ntb=0, igb=8, cut=999.0, rgbmax=15, ntpr=100, ntwx=1000, ntwr=100000,
nmropt=1, numexchg=1000, / &wt TYPE='END' /DISANG=m_chir.dat*
please let me know if you require any other details.
thanks
regards
chhaya
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Received on Mon Jul 09 2018 - 10:00:02 PDT
