AMBER Archive (2007)

Subject: AMBER: performance with implicit solvent

From: Kijeong Kwac (pine994_at_naver.com)
Date: Fri Jun 15 2007 - 15:02:49 CDT

Hello,
I am trying to do MD simulations of a large protein system with amber9.
What I would like to ask about is the performace of implicit solvent model compared to the explicit solvent.
The solute system has 2067 residues with 32566 atoms. When I did an amber run with the implicit solvent (cut = 12.0, igb = 5, gbsa = 1)
I got a trajectory of 17000 steps for 24 hours run (24 hrs = 86400 sec) using 4 cpus (2.66GHz intel dual core).
 
But, I also did the amber run with explicit water (39718 water molecules, total 151720 atoms).
then, I get a trajectory of 50000 steps for 38620.92 sec with the same machine.
 
Compare the two result:
 
Total # of atoms: 32566 (implicit), 151720 (explicit)
 
# of steps per hour: 708 (implicit), 4889 (explicit)
 
I am wondering why the implicit solvent method take much more time than with the explicit water.
Is this situation normal? Or, could there be something wrong?
 
 
The following is input for the explicit solvent run:
 &cntrl
 irest = 0, ntx = 1,
 nstlim = 50000, dt = 0.002, nsnb = 10,
 ntt = 1, tempi = 0.0, temp0 = 298.0,
 cut = 9.0, scee = 1.2,
 ntb = 1,
 ntf = 2, ntc = 2,
 ntwx = 200,
 ntr=1, restraint_wt=10.0,
 restraintmask='@1958,4028,6574,8644,11190,13260,15806,17876,20422,22492,25038,27108,29654,31724'
 &end
 
The following is input for the implicit solvent run:
&cntrl
 imin = 0, irest = 0, ntx = 1,
 nstlim = 200000, temp0 = 298.0, dt = 0.001,
 ntwr = 0,
 tempi = 298.0,
 ntt = 3, gamma_ln = 1,
 cut = 12.0, igb = 5, gbsa = 1,
 ntb = 0,
 ntf = 2, ntc = 2,
 ntwx= 250, nscm = 0,
 ntr=1, restraint_wt=10.0,
 restraintmask='@1958,4028,6574,8644,11190,13260,15806,17876,20422,22492,25038,27108,29654,31724'
 /
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