Dear AMBER users,
I am trying to run an equilibration md of a system
solvated in TIP3P waterbox. I wish to decrease the
restraints on the molecule in steps. In the first
cycle the system is heated up to 300K in 10ps. In the
next cycle I want to reduce the restraint force. But
when I do this the initial temperature is much
large(447.92K). My input files are attached. Please
look into this and suggest what is wrong.
Thanking you,
Mathew
i/p for the first step
-------------------------------------------------------
ade bulge: 10ps MD with res on DNA
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000,
nmropt = 1,
/
&wt type = 'TEMP0', istep1 = 0, istep2 = 50000,
value1 = 0.0, value2 = 300.0,
/
&wt type = 'END'
/
Keep DNA fixed with weak restraints
10.0
RES 1 17
END
END
-------------------------------------------------------
input I tried for the second step
-------------------------------------------------------
ade bulge: 10ps MD with res on DNA 5kcal
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000,
/
Keep DNA fixed with weak restraints
5.0
RES 1 17
END
END
--------------------------------------------------------
/\/\athew
Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India
email mathew_kvarghese.yahoo.co.in
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Received on Sat Sep 03 2005 - 07:53:01 PDT
