David A. Case wrote:
>On Tue, Nov 08, 2005, John S Zintsmaster wrote:
>
>
>>i'm am trying to calculate time correlation functions with amber 8 and i
>>am running into major brick walls. has anyone out there successfully
>>calculated a time correlation function via ptraj? is it possible? if so,
>>i would very much like to here about your experience.
>>
>>
>
>I do this all the time. But without knowing what problems you have, I don't
>see how I can help much.
>
>...dac
>
hello dr. case,
this was my description of the trouble i'm having:
*************************************************************************************
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
********************************************************************************
i've tried the above on different machines with excessive memory and get
the same seg. fault. the above ref. to a line in actions.c is where i've
stumbled to explain the seg fault. i have no clue if its a valid cause
at all. thanks a lot for any help.
John Zintsmaster
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Received on Tue Nov 08 2005 - 18:53:01 PST
