The first column denots the target distance between the two atom (or plane
or system of interest), second column shows the actual distance between
these two, third column represents the force on SMD atom while the last and
fourth column denotes the work done by the SMD atom.
For more information you can see the AMBER advanced Tutorial 26 section 2:
http://ambermd.org/tutorials/advanced/tutorial26/section2.html
On Wed, 14 Apr 2021, 06:56 吴晓东, <18xdwu.stu.edu.cn> wrote:
> Dear all,
> I run SMD by using Amber 20. In my inputfile, I have set some parameters
> of SMD to tell Amber run SMD.(As shown below) Then, in the output file,
> this simulation can be run successfully. I can get a file called
> "dist_vs_t". There are four columns of data in this file, but there is no
> title. So I don't know what these four columns mean?
>
> Input file:
> Sample pulling input
> &cntrl
> irest=1,ntx=5,
> nstlim=2000000,dt=0.002,
> igb=0,cut=8.0,
> temp0=300.0,
> ntt=3,gamma_ln=5.0,ig=-1
> ntc=2,ntf=2,
> ntpr=500,ntwx=2000,ntwv=0,ntwe=0,ntwr=2000,ntxo=1,iwrap=1,
> ntp=1,ntb=2,pres0=1.0,taup=1.0,
> ipol=0,tol=0.000001,
> jar=1,
> /
> &wt type='DUMPFREQ', istep1=1000, /
> &wt type='END', /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LISTOUT=POUT
> &end
>
> part of "dist_vs_t" file:
> 20.00000 27.77854 -155.57088 0.00000
> 19.99250 20.90928 -18.33554 0.20942
> 19.98500 20.31221 -6.54418 0.33826
> 19.97750 20.59676 -12.38525 0.42623
> 19.97000 20.56992 -11.99845 0.51276
> 19.96250 20.58287 -12.40731 0.60586
> 19.95500 20.29244 -6.74885 0.67079
> 19.94750 20.11455 -3.34104 0.72849
> 19.94000 20.43368 -9.87369 0.77824
> 19.93250 20.50480 -11.44597 0.83712
> 19.92500 20.19394 -5.37885 0.88489
> 19.91750 20.23326 -6.31521 0.93860
> 19.91000 20.17231 -5.24618 0.99481
> 19.90250 20.29418 -7.83359 1.05912
> 19.89500 20.16178 -5.33550 1.12539
> 19.88750 20.22177 -6.68550 1.18156
> 19.88000 19.89602 -0.32037 1.20717
> 19.87250 19.86138 0.22239 1.23157
> 19.86500 19.89926 -0.68510 1.26951
> 19.85750 19.86857 -0.22145 1.28906
> 19.85000 20.13551 -5.71029 1.30536
> 19.84250 19.92319 -1.61371 1.31613
> 19.83500 20.04631 -4.22625 1.33696
> 19.82750 20.12122 -5.87431 1.36713
> 19.82000 20.19494 -7.49889 1.39766
> 19.81250 20.15444 -6.83887 1.43710
> 19.80500 20.14334 -6.76681 1.45405
> 19.79750 19.86496 -1.34912 1.48940
>
> I analyzed the resulting data according to the tuition of T. Dwight McGee
> Jr. et al. I can get results similar to his. (the white is belong to T.
> Dwight McGee Jr; and black is mine) However, I still don't know what the
> second column of data represents in this document.
>
> I want to ask the meaning of each column of data in these output files.
> And how can I do it in order to correctly analyze the results of SMD.
> [cid:95bdfeb8-8a05-4efb-a9da-92b55fd69c3a]
> [cid:ed5031ad-61c2-4e72-89e1-4aab66716bda]
>
> Thanks,
> Xiaodong
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 13 2021 - 19:30:01 PDT
