[gmx-users] cannot print velocity information to trr/xtc files (Carbon Nanotube inside water)
robert.shelley at gmail.com
Wed Jul 23 21:29:29 CEST 2008
I am to accelerate water while freezing another group and would like to know
velocity information as has been posted before and was wondering if a
solution to the problem has been found.
Nadir Kaplan wrote:
>>> What is going on here? How can I get velocity info? Any help will be
>>> greatly appreciated. Note that, there is an external acceleration on
>>> the water molecules, where is the position of CNT is fixed. So
>>> obviously water molecules should have finite velocities.
>> Turn off the weird stuff (freeze groups and accelerate groups) until
>> you've got your basic issues sorted out. MD simulations in general and
>> CNT simulations in particular are not easy things to do right. Learn
>> to walk before you try to run! :-)
> Freezing is for simplicity. One needs velocity to run.
Yeah, but freezing and accelerating do things to velocities. If you're
having problems, a good strategy is to simplify the situation until you
can identify where the problem arises... thus, no freezing and accelerating.
> Below I paste another mdp file which I used for the MD part of the same
> simulation. That MD simulation was succesfully over and I was able to
> reproduce some results in the literature by using position info. Again,
> in the .trr file of that simulation, there are no velocities.
Well, those reproduced results probably mean that there *were*
velocities :-) Velocities must be there in the .trr for the last
timestep, so long as mdrun was allowed to terminate normally.
If you really had "nstvout = 5000" and you are looking at the correct
non-post-processed trajectory with gmxdump on a suitable timestep, then
your observations are inexplicable, unless there's some weird "gotcha"
with no velocities being written for atoms in either a freeze or
accelerate group... not that that makes much sense... In short, it seems
much more likely you've made an error than that there's a weird bug.
My earlier advice is still good - get a clean working directory and do
the same kind of simulation but without the freeze and accelerate groups
and see if you can reproduce your problem while recording everything you
did on the way. If it now works, do the same but add in the weird stuff
until you isolate the problem - if any.
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