[AMBER] Force/Energy vs extension curve from Steered MD

From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Date: Sat, 25 Mar 2017 17:36:15 +0000

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 and I have also attached my dist.dat output 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 - 11:00:02 PDT
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