Hi,
Hai's advice on upgrading is probably your best bet. The 'radial'
command can be very time consuming since many distances (and in this
case imaged ones) need to be calculated each frame, so you may want to
use the OpenMP-parallelized version of cpptraj (cpptraj.OMP) as well.
-Dan
On Fri, Aug 4, 2017 at 5:18 PM, Christopher Gorman <cbgorman.ncsu.edu> wrote:
> Hi, I'm trying to compute the radial distribution function (RDF) of
> selected atoms in the dendrimer with respect to the center of mass in the
> molecule. I have executed the cpptraj commands below, but the program just
> hangs (non-responsive for > 15 min). I think I have the correct syntax but
> I guess not. Can anybody help me out?
>
> Also, what is "imaging"? I can't find a definition in the ambertools
> manual.
>
> [cbgorman.login03 cbgorman]$ cpptraj
>
> CPPTRAJ: Trajectory Analysis. V12.4
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
>> parm G3-dox-OH.prmtop
> [parm G3-dox-OH.prmtop]
>> trajin G3-dox-OH-prod-nice.crd
> [trajin G3-dox-OH-prod-nice.crd]
> [G3-dox-OH-prod-nice.crd] contains 100 frames.
>> strip :WAT
> [strip :WAT]
>> radial G2.rdf 0.5 20 :* :6-13.N4 center1
> [radial G2.rdf 0.5 20 :* :6-13.N4 center1]
>> go
>
> INPUT TRAJECTORIES:
> [G3-dox-OH-prod-nice.crd] is an AMBER trajectory, Parm 0 (reading 100 of
> 100)
> Coordinate processing will occur on 100 frames.
>
> PARAMETER FILES:
> 0: G3-dox-OH.prmtop, 29388 atoms, 9389 res, ortho. box, 9329 mol, 9328
> solvent mol, 100 frames
>
> REFERENCE COORDS:
> No reference coordinates.
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> ACTIONS: Initializing 2 actions:
> 0: [strip :WAT]
> STRIP: Stripping atoms in mask [:WAT]
>
> 1: [radial G2.rdf 0.5 20 :* :6-13.N4 center1]
> RADIAL: Calculating RDF for atoms in mask [:*] to atoms in mask
> [:6-13.N4]
> Output to G2.rdf.
> Using center of atoms in mask1.
> Histogram max 20.000000, spacing 0.500000, bins 40.
> Normalizing using particle density of 0.033456 molecules/Ang^3.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [G3-dox-OH.prmtop]: Setting up 2 actions.
>
> 0: [strip :WAT]
> Stripping 27984 atoms.
> strip.G3-dox-OH.prmtop: Setting up 1423 bonds.
> Topology contains 1404 atoms.
> 61 residues.
> 1423 bonds.
> 1 molecules.
> 1: [radial G2.rdf 0.5 20 :* :6-13.N4 center1]
> RADIAL: 1404 atoms in Mask1, 8 atoms in Mask2, Imaging on.
> ----- [G3-dox-OH-prod-nice.crd] (1-100, 1) -----
> 0%
>
> --
> ------------------------------------------------------------------
> Christopher Gorman, Professor of Chemistry
> Department of Chemistry 919-515-4252 (office)
> North Carolina State University 919-515-8920 (fax)
> Box 8204 919-515-8918 (lab)
> Raleigh, NC 27695-8204 Chris_Gorman.ncsu.edu
> Use 45 Dabney Hall instead of Box 8204 for Express Deliveries
>
> Learn about the Gorman group on the WEB:
> http://www4.ncsu.edu/~cbgorman
> ------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Aug 07 2017 - 09:00:03 PDT
