Dear all,
For polyAT_wat_md1.in
(
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section5.htm):
polyA-polyT 10-mer: 20ps 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 = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep DNA fixed with weak restraints
10.0
RES 1 20
END
END
I have a question on the temperature increasement.
First of all, for initial temperature 0 K, it cannot
reflet the real system, because a real system can
never has a frozen temperature. Is the parameter
initial T=0 correct or not?
Secondly, for this md, the total length will be 20 ps.
How long does it to take to increase the temperature
from 0K to 300K?
I am looking forward to getting your reply.
Best regards.
Fenghui Fan
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Received on Sun Sep 17 2006 - 06:07:05 PDT
