Justin A. Lemkul wrote:
Quoting Mark Abraham <[EMAIL PROTECTED]>:
Itamar Kass wrote:
Thank Justin,
Still I am wondering about the grompp option, 'cause this is what I use
most. You my also say I am invested in this (in CPU time manner).
You being cryptic doesn't serve your purpose of getting useful free help
:-)
Justin's advice was correct but incomplete, in that grompp also has a
-time option you can use. The advice on the URL he provided will answer
both this and your other questions, as would reading the GROMACS manual
and/or man page :-)
Thanks for pointing that out Mark, but I am wondering if you (or anyone else out
there) might be able to clear up a little confusion I have (and hence the reason
I have always used tpbconv if my .edr and .trr don't match up for whatever
reason). Does the tinit option in the .mdp file override the -time argument,
in the same way that gen_vel = yes would override the velocity input from the
.trr? The manual and online documentation don't seem to give me a clear answer
to this question.
I haven't tested that one... tinit overrides the time of the last
useable frame if you don't supply -time, so I'd have to suppose it works
the same way if the frame is specified with -time. If this were not
true, then tinit would be constrained to be a time in the supplied
trajectory. This kind of thing would be easy to check with some quick
changes to .mdp and/or command line and comparison of the output .tpr
with gmxcheck -s1 -s2.
If you do this, please report what you see and I'll update the wiki page.
I suppose it would be just as easy to remove any reference to tinit in the .mdp,
but in any case I'm curious.
Mark
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