Dear Amber User's
I am simulating a small peptide ( Trpcage peptide in water) through T-REMD.
The system details given below
1) The total no of atoms = 6302 (Peptide = 20 amino acid, water = 2000)
2) Temperature range 290 to 600
(I used this web server <
http://folding.bmc.uu.se/remd/>to predict
temperature of each replica)
3) Total no of replica = 64 and no of CPU = 64
4) Input file
&cntrl
imin = 0, ntx = 5, irest = 1,
nstlim = 500, dt=0.002, cut=10.0,
ntpr = 1000, ntwx = 1000, ntwr = 1000, ioutfm = 1,
ntc = 2, ntf = 2, ntxo = 2, iwrap=1,
ntb = 1, tautp = 2.0, ig= RANDOM_NUMBER,
tempi = XXXXX, temp0 = XXXXX, ntt =3, gamma_ln = 1,
ntp = 0, numexchg = 15000, nmropt=1,
&end
&wt TYPE='END'
&end
&ewald
EW_TYPE=1
&end
DISANG=trpcage_wat_leap.CHIR.dat
Now I have two question
1) Is there a way to improve performance of this REMD simulation. I am
getting only 0.11 ns/day on 64 CPU.
| Current Timing Info
| -------------------
| Total steps : 2500000 | Completed : 2077000 | Remaining : 423000
|
| Average timings for last 1000 steps:
| Elapsed(s) = 1562.38 Per Step(ms) = 1562.38
| ns/day = 0.11 seconds/ns = 781189.58
|
| Average timings for all steps:
| Elapsed(s) = 3256969.81 Per Step(ms) = 1568.11
| ns/day = 0.11 seconds/ns = 784056.29
|
| Estimated time remaining: 184.3 hours.
2) Could I run multiple systems to generates large no of trajectory. My
objective for this simulation is study stability and folding and unfolding
of Trpcage protein in water (Similar to
http://www.pnas.org/content/105/46/17754.full ).
Thank you very much for valuable suggestion
Regards
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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Received on Wed Jun 07 2017 - 14:00:02 PDT
