> I emailed yesterday about tracking a water molecule. I have created
> water trajectories using "closest" ("closest 3 :557.NH1 oxygen") command
> in ptraj. This seems to work fine. I get a mdcrd output of the
OK, note that the closest waters change over the course of a simulation
(i.e. the closest ones are not necessarily the same water molecule over
the course of the trajectory) so that this is different than "tracking"
a specific water model.
> trajectories. However, when I try to measure the distance between
> residue 557.NH1 to the first water oxygen over the trajectories I get
> this error: "./ptraj Memory fault".
>
> Trajin File.mdcrd
> Distance one time 5 :557.NH1 :1.O file.txt
Usually the waters come after the solute so I think what is causing the
core dump is that residue 1 (:1) does not have a "O" atom in it.
Note that if you simply want to track waters close to that residue, you
can use the hbond facility:
donor mask :557.NH1
hbond series hb out hbond_wat.out \
solventacceptor WAT O H1 \
solventacceptor WAT O H2 \
time 5.0 angle 120.0 distance 3.5
[In principle you could add (before the hbond command):
acceptor WAT O H1
acceptor WAT O H2
...but this may blow memory if you have lots of water; however if it does
not, this would be a way to track "which" water molecules are interacting
when, although I do not know how useful this is...]
-- tec3
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Received on Sun May 04 2008 - 06:07:41 PDT
