Dear Amber users
I have run steered MD using jar=1 to extend a dodecamer DNA duplex from 40 A0 to 110 A0 using explicit solvation TIP3PBOX. But I do not understand how to plot force vs Extension? Is it the column 3 vs column 1 of the dist_vs_t output file? When I plot this, it gives something wrong for certain.
Beside force vs extension, I thought that column 4 vs column 1 of the dist_vs_t output file gives me the plot for energy vs extension, but it gives something totally wrong. How can I plot energy vs extension curve? Even I took the derivative of column 4 vs column 1 to give me the force vs extension curve, but it did not give me the expected plot.
Do I need to use GB/SA implicit solvation method to plot energy vs extension? But how am I supposed to factor in GB/SA model while I have used explicit solvent?
Knowing that the jar option internally turns on nmropt, what is the difference between using nmropt=1 and jar=1 to do the steered MD? Are they supposed to give similar force/energy vs extension curves?
The following is my input file:
imin = 0, nstlim = 800000, dt = 0.002,
ntx = 5, tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln=5.0
ntc = 2, ntf = 2, ntb = 2, ntp = 1,
ntwx = 100, ntwr = 100, ntpr = 100,
ntwv = 100, ntwf = 100, ntwe = 100,
cut = 8.0, ig=-1, ioutfm=1,
irest = 1, jar=1,
/
&wt type='DUMPFREQ', istep1=1000 /
&wt type='END' /
DISANG=dist.example.RST
DUMPAVE=dist.smd3.dat
LISTIN=POUT
LISTOUT=POUT
/
&rst
iat=2,382,
r2=40,
r2a=110,
rk2=50,
&end
Thanks in Advance
Ramin Salimi
Graduate Research Assiatant
Department of Physics
University of Texas, Rio Grande Valley
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Received on Sat Mar 25 2017 - 11:00:03 PDT
