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

Junqiao Lee aeondrift at gmail.com
Wed Dec 24 14:11:38 CET 2008

Hi Mark,

>> Thanks for the help. I've tried both ways and both seem to work; with
>> the dash or the underscore...
>> Funny thing is that the grompp output seem to indicate that there are
>> 2 XTC elements (Protein rest) when I've set xtc_grps = Protein.
>> 1 XTC element (rest) when not setting xtc_grps to any specific groups
>> (i.e. default).
>> 1 XTC element (Protein) when setting xtc_grps = Protein SOL or Protein
>> Non-Protein ...etc.
>> Again, I'm currently using Gromacs/3.3.3
> Your use of "seems" suggests to me that you haven't actually done an
> experiment controlling all variables except the spelling of the name of
> this option and the names of the groups you're giving. As such, your
> observations don't help anybody much :-)

> You can use gmxcheck to compare pairs of run input files, which can be
> useful here.

You're right, I've only did what as you've said, and what I've earlier
described. I've concluded based only from the respective outputs from
grompp and the subsequent mdrun, but I was puzzled by how the grompp
outputs did not "seem" to correspond to what I fed it via my
mdp-inputfile; as mentioned in my previous post above. But grompp
certainly does "respond" to both xtc-grps and xtc_grps, and is
correctly placed (under the correct ;heading/label) within the
generated mdout.mdp file as xtc-grps or xtc_grps respectively,
dependant on how it was specified in the inputfile that I've fed it.

Anyhow I certainly well post-up any interesting results when I do a
more thorough check(s) of these variables. ;)

> The file produced by mdrun -c contains the whole simulation system
> regardless. The file produced by mdrun -x contains the groups, data
> types and frequencies indicated in the corresponding .mdp file options.

Thanks, this cleared it up for me.

>> visualise it, the solvent molecules (all ~7800 of them) was found to
>> be still there. And loading the .xtc file to the molecule, I can see
>> both the protein and solvents were moving, which seem to indicate to
>> me that the .xtc file actually contains data for the whole system
>> basically (instead of just the protein). This was what had confused
>> me.

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?

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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