[gmx-users] Re: Saving trajectories of a particular group within the system.

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 24 14:25:22 CET 2008

Junqiao Lee wrote:


> Since the .xtc file does not contain any trajectory data for the
> solvents, I've assumed that the water molecules when visualised using
> VMD should not be moving. Would that be correct?

No, VMD will give an error if you load a stucture file followed by an .xtc that 
does not contain the same number of atoms.


> It is plausible that I might have done it wrong perhaps, I'll check
> one more time again tomorrow when I get back to my Uni.
>>> correct? Or is there some misunderstanding on my part. I've read the
>>> manual as carefully as I can, but as a human, I might still make
>>> mistake or interpret what it say wrongly. Hencefore, I need to
>>> cross-check before I initiate the (much longer) real simulation; since
>>> what I've seen with VMD looked a bit "dodgy" as mentioned above.
>> The lesson here is to read carefully, and experiment carefully. If you
>> don't know what you've varied, then your observations will be confused,
>> just like in real laboratory science :-) In the experience of a lot of
>> competent people, all these options work as described, and you need to
>> be on very strong ground to suggest they don't! :-)
> Do pardon my bad use of words. In no way was I implying that I though
> it was a problem with gromacs itself, but rather I was suspecting that
> I might had overlooked something and not done things correctly...etc
> ;)
> Earlier I had problems with getting my system to solvate properly with
> my tip4p solvents, and also during my introduction of counter-ions
> into my system. I had finally gotten them fix through trial and error,
> by "messing around" with the various files. So I thought that might
> also have been the case, i.e. that I need to do something more to get
> it to work.
> Thanks for clearing things up Mark.
> That helped, I feel more confident and have submitted a 1 ns
> simulation and see how it goes.
> Merry Christmas,
> (Wade) Junqiao Lee
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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