Dear all,
I carried out two simulations on the same RNA molecule using both AMBER 8
and AMBER 7.
I used exactly the same input files, just changing the Temperature control
method.
I run two equilibration steps using the input files pr.in and em.in
(please, see below). Then I slowly heated the sistem at 300K using the
input file md1.in and then I rund 10ns of unrestrained MD.
Surprisengly the minimized structures look very diffent and the
unrestrined MD trajectories show a very different behaviour: I obtained a
very stable trajectory using AMBER 7 and an instable one using AMBER 8.
How may I solve this mistake?
Many thanks in advance,
Vincenzo
1)pr.in
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 1,
ntr = 1,
cut = 10
/
Hold the RNA fixed
500.0
RES 1 24
END
END
2)em.in
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 10
/
3)md1.in
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 1, (I used ntt = 3 in AMBER 8)
tautp = 0.2, (I used gamma_ln = 1.0 in AMBER 8)
nstlim = 10000,
dt = 0.002,
ntpr = 500,
ntwx = 500,
ntwr = 1000
/
Keep RNA fixed with weak restraints
10.0
RES 1 24
END
END
4)md2.in
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
pres0 = 1.0,
ntp = 1,
taup = 2.0,
cut = 10,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 1, (I used ntt = 3 in AMBER 8)
tautp = 0.2, (I used gamma_ln = 1.0 in AMBER 8)
nstlim = 5000000,
dt = 0.002,
ntpr = 500,
ntwx = 500,
ntwr = 1000
/
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Received on Sun Mar 05 2006 - 06:10:17 PST
