Hi
Thanks for the reply.
Because I am trying to reproduce the results of a paper and their plots are totally different than mine. The following is the paper I am referring to:
Molecular Dynamics Simulations of Duplex Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA
Sarah A. Harris,* Zara A. Sands, and Charles A. Laughton
In the paper, the authors use GB/SA model to plot energy vs Extension curve and take the derivative of that with respect to the extension to get force vs extension curve. But I am so confused why we need to implement GB/SA? We did everything with TIP3PBOX. Additionally, if you look at Fig. 2 and 3 in the paper, it looks to me that they have pretty much, not completely, the same behavior, and one cannot be the derivative of the other; which is the characteristics of the exponential function, which caused me think that they might have been plotted out of different data sets.
Thanks
Ramin Salimi
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Saturday, March 25, 2017 1:03:39 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Force/Energy vs extension curve from Steered MD
Hi
Can you explain why do think this is wrong ?
Thanks
On 3/25/17 1:36 PM, Ramin Salimi wrote:
> 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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Sat Mar 25 2017 - 11:30:03 PDT
