[gmx-users] Re: gmx-users Digest, Vol 56, Issue 74

Junqiao Lee aeondrift at gmail.com
Wed Dec 24 10:06:46 CET 2008

Hi Jeroen, Tsjerk,

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

However, looking at the size of the output-files, xtc_grps = Protein
seem to be correct.
The other two generated much bigger .xtc files.

As previously indicated, I'm only interested the the various
structural conformations adopted by the protein-molecule as it samples
across the potential landscape during a very long simulation (> 10ns
perhaps in steps of 1ns). I intend to output the coordinate
trajectories at very short time-intervals of 50 fs. i.e. Infact, I
only need the coordinate data of the protein during the
virtual-cooking period, and not the velocities of the protein, and
none of the data of the solvent (+ counter ions) molecules.

The relevant section of the current .mdp input-file settings I've made
is as follows:-

nstcomm                  = 10
comm-mode                = Linear

xtc-grps                 = Protein
nstxout                  = 10000
nstvout                  = 10000
nstfout                  = 0
nstxtcout                = 50

nstlog                   = 1000
nstenergy                = 1000

nstlist                  = 10
ns_type                  = grid


I'm wondering if by setting xtc_grps = Protein, am I to expect the
generated .g96 and .xtc file (after mdrun have completed the full
simulation) to contain data particular to the Protein only, which was
what I was hoping for? However, loading the .g96 file into VMD to
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

However, I've just realised that the .xtc file does seem to be much
smaller, after performing the short test runs to compare.

Just to verify, by setting xtc_grps = Protein, what should I expect
with the various files (.xtc, .trr, etc.). Should I expect the
simulation to throw out trajectories of the Protein group only to the
.xtc file at time-interval set by "nstxtcout" (fs). While "nstvout"
and "nstxout" sets the data to output to the .trr file, would that be
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.

I've set "nstxout" and "nstvout" to a much larger time-interval, as
the .trr file-size tends to blow up rather quickly (because its not
compressed?), and I'm assuming those two parameters are with regard to
the .trr output and not the .xtc output during the simulation.
Does my .mdp file above, correspond to what I'm intending to achieve
(as described above - i.e. saving only the trajectories of the protein
during the simulation)? Any suggestions for perhaps better way of
doing it would be helpful too. =)

Hope I've provided sufficient information for you to "go with" and
that its not too confusing to read and get what I'm trying to say,
English isn't really my mother tongue and sometimes I can be a bit
confusing no matter how hard I try to articulate myself
properly/clearly. Further, hope I've not annoyed anyone too much by
asking stupid questions. I'm new to the MD thing and I've just started
working on this as a short 10-weeks internship, after having completed
my degree in Nanotechnology (i.e. Physics, Chemistry major), as I find
this project interesting.

Thanks for all the help! And have a merry Christmas. =D


> Hi Tsjerk,
> So the claim in the online manual (under
> http://www.gromacs.org/documentation/reference_3.3/online/mdp_opt.html#g
> eneral), that "the difference between a dash and an underscore is
> ignored", is incorrect according to you? Or is it only incorrect for the
> option "xtc-groups"?
> If incorrect I'd say this should be changed asap. But actually I believe
> it is correct, at least for the options I've tried.
> Thanks,
> Jeroen


> Hi Jeroen, Wade
> I missed that one.., also in the source (haven't checked where it is
> in that case). But it seems you're right, and the original post then
> leavves me blue.
> Wade,
> Check the .mdp file that is generated by grompp, and see what it says
> for xtc-grps. Please report back to the list.
> Cheers,
> Tsjerk

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