Hello,
With a new test, It seem like a bug in the cpptraj when using center only for the solvent.
Without center2 :
radial Rad_M8_CLCen_NH_CHCl3_NoCen2.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3 volume
results are ok:
#Distance_(Ang) :2.H_=>_:CL3.CL1,CL2,CL3
0.050000 0.000000
0.150000 0.000000
0.250000 0.000000
0.350000 0.000000
0.450000 0.000000
0.550000 0.000000
0.650000 0.000000
0.750000 0.000000
0.850000 0.000000
0.950000 0.000000
1.050000 0.000000
1.150000 0.000000
1.250000 0.000000
1.350000 0.000000
1.450000 0.000397
1.550000 0.000000
1.650000 0.000613
1.750000 0.000272
1.850000 0.000244
1.950000 0.001316
2.050000 0.006947
2.150000 0.032482
2.250000 0.117318
2.350000 0.250289
________________________________________
De: JAIME RUBIO MARTINEZ
Enviado: miércoles, 21 de diciembre de 2016 17:20
Para: AMBER Mailing List
Asunto: Re: [AMBER] rdf_with_center_in_cpptraj_16
Hello,
Thanks for your suggestion....
Curiously, when the center is in the Ala residue results are ok.
radial Rad_M8_CH3_H1_CHCl3.txt 0.1 10.0 :2.CB,HB1,HB2,HB3 center1 :CL3.H1 volume
But with :
radial Rad_M8_CLCen_NH_CHCl3.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3 center2 volume
I have different results ... but the same error .......
source /home/prog/amber16/amber.sh
/home/prog/amber16/bin/cpptraj ./dialanine.top > Radial_M8_CHCl3.out << EOF
trajin ../minim_num_8_all.nc 1 last 1
autoimage
reference da_chcl3_reference_FIRST.pdb
rmsd reference out rmsd_ff14sb_wat_M8.dat :1-3.CA,N,C
radial Rad_M8_CLCen_NH_CHCl3.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3 center2 volume
go
EOF
#Distance_(Ang) :2.H_=>_:CL3.CL1,CL2,CL3
0.050000 0.000000
0.150000 0.000000
0.250000 0.000000
0.350000 0.000000
0.450000 0.000000
0.550000 0.000000
0.650000 0.000000
0.750000 0.000000
0.850000 0.000000
0.950000 0.000000
1.050000 0.000000
1.150000 0.610907
1.250000 0.000000
1.350000 1.330146
1.450000 1.921791
1.550000 15.137103
1.650000 45.418719
1.750000 124.299935
1.850000 297.317718
1.950000 561.793906
2.050000 847.220257
2.150000 1120.499190
2.250000 1193.650059
2.350000 1074.333347
________________________________________
De: Daniel Roe [daniel.r.roe.gmail.com]
Enviado: miércoles, 21 de diciembre de 2016 15:59
Para: AMBER Mailing List
Asunto: Re: [AMBER] rdf_with_center_in_cpptraj_16
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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--
-------------------------
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 Sun Dec 25 2016 - 10:00:02 PST
