Hi,
I want to do the molecular dynamics simulation between RNA-Protein complex
for 50 ns or 100 ns. For this I have used ff12SB force field as I am using
AMBER12 CUDA version. I have made three different input files for Heating,
Equilibration, and Production run. The input files are given below
respectively.
&cntrl
imin = 0,
ntpr = 500, ntwr = 100000, ntwx = 500, ntwe = 500,
ntf = 2, igb = 0,
cut = 10.0,
nstlim = 5000, dt = 0.002,
tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0,
ntb = 1, ntp = 0,
ntc = 2, tol = 0.00001,
vlimit = -1.0d0,
/
&ewald
vdwmeth = 1,
/
For Equilibration the input file is:
&cntrl
imin = 0,
ntx = 7, irest = 1,
ntpr = 500, ntwr = 100000, ntwx = 500, ntwe = 500,
ntf = 2, igb = 0,
cut = 10.0,
nstlim = 5000, dt = 0.002,
tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0,
ntb = 2, ntp = 1, taup = 10.0,
ntc = 2, tol = 0.00001,
vlimit = -1.0d0,
/
&ewald
vdwmeth = 1,
/
For Production run the input file is:
&cntrl
imin = 0,
ntx = 7, irest = 1,
ntpr = 500, ntwr = 100000, ntwx = 500, ntwe = 500,
ntf = 2, igb = 0,
cut = 10.0,
nstlim = 5000, dt = 0.002,
tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 10.0,
ntb = 1, ntp = 0,
ntc = 2, tol = 0.00001,
vlimit = -1.0d0,
/
&ewald
vdwmeth = 1,
/
Please reply me, can I use these parameters or it needs any modification?
I will be thankful to you.
Thanks and Regards,
Richa Anand
Research Scholar
IIIT Allahabad
India
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Received on Wed Feb 12 2014 - 20:30:02 PST
