Dmitry Lupyan wrote:
I'm not sure this information is in my trajectory, the axis in the
msd.xvg only goes up to 600ps (and not 60ns). Is there anyway i can
set the interval in the trr file?
Use gmxcheck to check the contents of the .trr file, which will include frame
interval. If it is wrong (i.e., a consequence of the conversion from NAMD ->
GMX), use trjconv -timestep.
-Justin
-dima
On Tue, Apr 14, 2009 at 6:05 PM, Justin A. Lemkul <[email protected]> wrote:
Dmitry Lupyan wrote:
Hello Gromacs Users,
I have a 60ns trr trajectory file (converted with VMD from namd2
trajectory) which has 6000 snapshots saved at 10 ps intervals. how do
I specify the snapshot interval to g_msd so it calculates the D
properly?
Which option are you referring to? The only one I can think of is
-trestart, which has nothing to do with frame interval, but is related to
statistics. You shouldn't have to tell any of the Gromacs tools what the
frame interval is; if you have a valid trajectory, that information is
already present.
-Justin
-dima
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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