Dear Amber Users
I have run a 10ns simulation using Amber12. The input file is
md, npt, equilibrium to 300K quickly,
&cntrl
imin = 0, ntx = 7, irest = 1,
ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
nstlim = 5000000, dt =0.002,
tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
&end
END
END
The output file shows that all the 5000000 steps were completed. However
when I load it in VMD (or even check it using cpptraj/ptraj), I notice that
only some 2000 odd frames are present. The same input file gives 5000
frames as expected for the subsequent 10 ns runs. Where am I going wrong?
Thanks in advance for your help.
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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Received on Tue Aug 25 2015 - 00:30:03 PDT
