Date: Fri, 10 Jul 2015 10:20:43 -0400
Dear Amber !
I am doing a simulation of a protein complex.
the protein is having two chains A and B and a ligand.
I did md for 20 ns in NPT ., when I converted the final md.rst file to pdb
and viewed it
the protein chains split apart . what is the mistake I am doing
i used the following input file !
Molecular_dynamics for 5 ns
&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 = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwe = 1000,
iwrap=1
/
attached the image
comments will improve my understanding !
thank you !
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