Dear all Users!
I would like to perform molecular dynamic on a protein pore (3600 atoms) in
continuum with Amber 8.0.
My problem is with this system, the simulation seems to be very very long
(md1: 57 hours for 100ps). Is it normal?
Amber was compiled on AMD64 under Linux (Gentoo) and my input files are :
--------------------------------------------------
min1.in:
&cntrl
imin=1, maxcyc=1000, ncyc=500,
drms=0.05, igb=1,
ntb=0,
cut=12.0,
ntpr=100,
&end
-------------------------------------------------
md1.in
&cntrl
imin = 0,
irest = 0,
ntb = 0,
cut = 12, igb=1,
ntr = 1,
tempi = 300.0,
temp0 = 300.0,
ntt = 1,
nstlim = 100000, dt = 0.001,
ntpr = 100, ntwx = 100, ntwr = 100,
&end
Restraint on Pore (1-256)
0.5
RES 1 256
END
END
---------------------------------------------------
md2.in:
&cntrl
imin = 0,
irest = 1, ntx=5,
ntb = 0,
cut = 12, igb=1,
ntr = 0,
tempi = 300.0,
temp0 = 300.0,
ntt = 1,
nstlim = 400000, dt = 0.001,
ntpr = 400, ntwx = 400, ntwr = 400,
&end
------------------------------------------------------
I would like to know if the simulation time is normal and my methodology is
correct?
I performed already the Tutorial 2 to estimate the binding energy and my
simulation were ok.
Thanks in advance!!!!
BOLLOT Guillaume
Organic Chemistry Department
University of Geneva
30, quai Ernest-Ansermet
CH-1211 Geneva 4
tel. +41-22 379 6155
e-mail: Guillaume.Bollot.chiorg.unige.ch
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Oct 31 2005 - 08:53:00 PST
