hello,
i'm am trying to calc time correlation functions with ptraj and cannot.
i am getting a segmentation fault error when i try this.
here is my ptraj.in:
------------------------------------
trajin NVE.trj
trajout NVE_trajout
strip :WAT
vector v0 .14 corr .15 out v0.out
analyze timecorr vec1 v0 out v0_tcf.out
-------------------------------------
here is the majority of what comes out when i enter ~:ptraj BNZ.top
ptraj.in -
-------------------------------------
PTRAJ: Processing input file...
Input is from file ptraj.in
PTRAJ: trajin NVE.trj
Checking coordinates: NVE.trj
PTRAJ: trajout NVE_trajout
PTRAJ: strip :WAT
Mask [:WAT] represents 1644 atoms
PTRAJ: vector v0 .14 corr .15 out v0.out
Mask [.14] represents 1 atoms
Mask [.15] represents 1 atoms
PTRAJ: analyze timecorr vec1 v0 out v0_tcf.out
Segmentation fault
-------------------------------------
i have tried many variations of the input file. there seems to be a
memory allocation problem in the actions.c. when amber is run with
debugging flags a possible bug was identified . line 12067 in actions.c.
it seems that VectorInfo - Vx[i] Vy, Vz, Cx, Cy, Cz...etc
might be the root of the problem. has anyone had trouble with this
before (or have a solution). if i just try to use the vector comand and
try to dump the vector information to some .out i get a seg fault right
before it fills the .out file.
thank you for any guidance in this issue, it is greatly appreciated.
johnny
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
John S. Zintsmaster
mailing address:
251 Nieuwland Science Hall
Dept of Chemistry and Biochemistry
University of Notre Dame
Notre Dame, IN 46556
office: 162 Stepan Chemistry Hall
phone: 574-631-8864
dept fax: 574-631-6652
e-mail: jzintsma.nd.edu
website: www.nd.edu/~jzintsma
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Received on Mon Nov 07 2005 - 16:53:01 PST
