AMBER Archive (2009)

Subject: [AMBER] pmemd vs sander.MPI

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Nov 04 2009 - 11:32:05 CST

Hi
I am using sander.MPI to run a dynamics simulation with a restraint mask

Molecular Dynamics for 2ns - only Surface atoms are fixed
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
pres0 = 1.0,
ntp = 2,
taup = 5.0,
cut = 8.0,
ntr = 1,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ntt = 1,
iwrap = 1,
nstlim = 1000000, dt = 0.002
ntpr = 5000, ntwx = 5000, ntwr = 50000
restraint_wt = 20.0,
restraintmask = ':2',
/

can i run the above with pmemd by changing the last two lines
Molecular Dynamics for 2ns - only Surface atoms are fixed

&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
pres0 = 1.0,
ntp = 2,
taup = 5.0,
cut = 8.0,
ntr = 1,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ntt = 1,
iwrap = 1,
nstlim = 1000000, dt = 0.002
ntpr = 5000, ntwx = 5000, ntwr = 50000
/
Hold the surface fixed
20.0
RES 2
OR ATOM 51 1270?

Also, i do remember talking with Dr. Walker about pmemd being faster and
just as accurate as sander.MPI, is that also true when using 32 or 64
processors, or is it especially true when using large number of processors?

many thanks,
Taufik

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