Hi,
In general for 'radial' you want your first mask to have the most atoms. So try
radial Rad_M8_NH_CLCen_CHCl3.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3
center2 volume
instead and see if that helps.
-Dan
On Wed, Dec 21, 2016 at 8:01 AM, JAIME RUBIO MARTINEZ
<jaime.rubio.ub.edu> wrote:
> Hello,
>
> I am trying to calculate RDF with cpptraj ( amber16 ) for Dialanine in chloroform.
>
> 1) The results when using this expression seem to be ok:
>
> radial Rad_M8_CH3_CLCen_CHCl3.txt 0.1 10.0 :2.CB,HB1,HB2,HB3 center1 :CL3.CL1,CL2,CL3 center2 volume
>
> #Distance_(Ang) :2.CB,HB1,HB2,HB3_=>_:CL3.CL1,CL2,CL3
> 0.050 0.000000
> 0.150 0.000000
> 0.250 0.000000
> 0.350 0.000000
> 0.450 0.000000
> 0.550 0.000000
> 0.650 0.000000
> 0.750 0.000000
> 0.850 0.000000
> 0.950 0.000226
> 1.050 0.000000
> 1.150 0.000155
> 1.250 0.000131
> 1.350 0.000075
> 1.450 0.000065
> 1.550 0.000057
> 1.650 0.000100
> 1.750 0.000134
> 1.850 0.000179
> 1.950 0.000233
> 2.050 0.000227
> 2.150 0.000324
> 2.250 0.000444
> 2.350 0.000506
>
> However this other expression fails and I don't understant why :
>
> radial Rad_M8_NH_CLCen_CHCl3.txt 0.1 10.0 :CL3.CL1,CL2,CL3 center1 :2.H volume
>
> #Distance_(Ang) :CL3.CL1,CL2,CL3_=>_:2.H
> 0.050 0.000000
> 0.150 0.000000
> 0.250 0.000000
> 0.350 0.000000
> 0.450 0.000000
> 0.550 0.000000
> 0.650 0.000000
> 0.750 0.000000
> 0.850 0.000000
> 0.950 0.073139
> 1.050 0.239525
> 1.150 1.997049
> 1.250 8.663635
> 1.350 28.408471
> 1.450 86.507489
> 1.550 212.667108
> 1.650 434.138973
> 1.750 763.129547
> 1.850 1130.629447
> 1.950 1385.868655
> 2.050 1439.241063
> 2.150 1242.488203
> 2.250 892.349340
> 2.350 539.441398
>
>
>
>
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>
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>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Dec 21 2016 - 07:00:03 PST
