thank you for replying to my problem
I'm using amber8 and ther PTRAJ version therein
the rdf command that i used:
radial rdf.out 0.05 20.0 :WAT.O :1-10.CA
the problem starts here:
PTRAJ: Processing input file...
Input is from standard input
PTRAJ: trajin rty.15.crd.gz
Checking coordinates: rty.15.crd.gz
PTRAJ: radial rdf.out 0.05 20.0 :WAT.O :1-10.CA
Mask [:WAT.O] represents 3198 atoms
Mask [:1-10.CA] represents 10 atoms
FYI: No output trajectory specified (trajout), none will be saved.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 1000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (rty.15.crd.gz) is an AMBER trajectory (with box info) with 1000 sets
OUTPUT COORDINATE FILE
NULL entry
ACTIONS
1> RADIAL DISTRIBUTION FUNCTION: Output to rdf.out
spacing is 0.050
maximum is 20.000
[This implies 399 bins]
density is 0.033
RDF will bin all solute-mask to solvent-mask distances
Solvent atom selection is :85-3282.O
Solute atom selection is :1-10.CA
Processing AMBER trajectory file rty.15.crd.gz
Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500 .................................................
Set 550 .................................................
Set 600 .................................................
Set 650 .................................................
Set 700 .................................................
Set 750 .................................................
Set 800 .................................................
Set 850 .................................................
Set 900 .................................................
Set 950 .................................................
Set 1000 Segmentation fault (core dumped)
and the whole thing crashed
please help me, I think there is soemthing wrong with my trajectory, but i dont know what is it, because when i try using larger delta r, it works fine.
would somebody pls tell me what would be the possible problem?
and would somebody explain or suggest a paper/book/article that explains the effect of the width of the bin on this program,
thanks a bunch!!
Thomas Cheatham III <tec3.utah.edu> wrote:
> i need help on calculating rdf for my system using PTRAJ
...
> radial rdf.out 0.05 10.0 :WAT.O :7.CA
>
> if i used 0.05 as the width of the bin, the program
> crashed (core dumped)
I am not able to reproduce this with my amber9 version of ptraj or with
the older ptraj available on the WWW; what version are you using? Where
is it core dumping (before or after reading in all the frames)?
-- tec3
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Received on Wed Jun 20 2007 - 06:07:03 PDT
