> When series option is given the program continuously
> gives an error message
>
> Set 1 ..WARNING in ptraj(), hbond: Too many
> solvent acceptors near donor atom 17! (set
> solventneighor higher)
Right, what is happening is that for your given donor (atom 17) there are
more solvent acceptors found than the program can handle and the comment
says, increase solventneighbor (which is an option to the hbond command).
If you increase solventneighbor, you can avoid this error...
> I set the solventneighbor 15. then also the same error
> message is obtained.
If the same error message is obtained, it means that more than 15 solvents
are within range. You can either decrease the distance cutoff for hbond
or increase solventneighbor even higher.
> But when the series option is avoided, the program
> executes without any error messages.
This does not mean it is "correct". The series command is necessary to
understand any time dependent averages,
> I have tried to calculate the radial distribution
> functions. The program executes without any error
> messages and the output files are written out, but the
> programexits with a line,
> -------------------------
> Segmentation fault.
> -------------------------
This is unfortunate.
> How can I use the 3column data obtained from the
> radial
I would guess that it doesn't always segfault if you have the file to
view. The three oolumns are spacing, RDF and its integration (occupancy).
You can look at that xmgr file by simply ignoring the third column...
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Received on Fri Nov 18 2005 - 05:53:00 PST
