Re: [AMBER] rdf_with_center_in_cpptraj_16

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 6 Mar 2017 08:21:05 -0500

Hi,

Sorry for the long delay on this. I've unfortunately only just gotten
to it. After looking at your issue again I realized I overlooked
something very important the first time - the mask ':CL3.CL1,CL2,CL3'
selects multiple molecules. The 'centerX' keywords specify that you
want the RDF calculated with respect to the center of *all* atoms in
the mask. This means that you're taking the RDF with respect to the
center of everything selected by that mask. I think that maybe you
were expecting the center of *each*, is that right? So I think that
cpptraj is working as intended here. Let me know if I've missed
something.

Thanks,

-Dan

On Sun, Dec 25, 2016 at 12:54 PM, JAIME RUBIO MARTINEZ
<jaime.rubio.ub.edu> wrote:
>
> 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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-- 
-------------------------
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 Mon Mar 06 2017 - 05:30:03 PST
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