Dear All,
I am using amber9 to run MD of a small DNA duplex solvated in POL3 water model.
First, I minimized WAT and counterions without any problem. Then, I run MD with restrained on DNA and I got an error message.
Input file is
=============
20ps MD with restrained on DNA
&cntrl
ntb = 2, ntp = 1,
ntc = 2, ntf = 2,
ntt = 3, cut = 9.0,
ipol = 1,
temp0 = 300.0, ntr = 1,
gamma_ln = 1.0,
nstlim = 20000, dt = 0.001,
ntpr = 1, ntwx = 1000, ntwr = 1
/
Fix DNA
1000.0
RES 1 8
END
END
=============
Here I tried to set ntpr=1 to see what happen. Please see attached file for the output.
Any suggestion, please?
Regards,
Xioling
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- application/octet-stream attachment: md.out
Received on Thu Jun 09 2011 - 08:00:03 PDT
