[gmx-users] WARNING 1 [file aminoacids.dat, line 1]

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Oct 31 09:15:48 CET 2008


Temperature coupling has nothing to do with having a protein or not.
Likewise, pressure coupling, time step, total simulation length,
temperature and a lot of other options have nothing to do with having
protein or not. These are all basic things of performing simulations.
Now, you followed a tutorial on simulation of a protein in solvent.
That is just a trodden path, which makes it easy to explain the steps
involved in MD, relevant for a large group of students/scientists.
Something like learning to drive. First take the quiet roads. And
don't think that right after you managed to drive your first round by
yourself you're ready to go off-road rally racing! You'll have to make
yourself acquainted with the meaning of different steps if you want to
do anything which is beyond the scope of the tutorial (protein in
water). There's a whole bunch of us who have quite a bit of experience
and may provide you with some pointers, but then you have to make sure
that you give the relevant information.
You've been posting quite a bit over the past few days, and still
nobody here knows what you're doing. You haven't told us. Only that
you don't have a protein. What do you have then? And how large is it?
Why should I ask you? This is not to express annoyance or anything,
but please bear in mind that you're not the student of any of us, and
we're not paid for trying to help you out. You're requesting free
help, so make it easy for us to help you.


On 10/31/08, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> Justin asked "Is this the only output?  What is the whole output of the
> command?"
>  And while you did post the entire output, one might notice that the actual
> warning has nothing to do with protein/non-protein.
>  WARNING 1 [file aminoacids.dat, line 1]:
>  T-Coupling group azoct has fewer than 10% of the atoms (33 out of 3660)
>  Therefore, no, you should not ignore this warning. Change your temperature
> coupling groups to something more reasonable. Generally, that would mean
> join the smallest group with one that makes sense. Sure, 10% is an arbitrary
> selection, but there is a lot to be careful about here.
> http://wiki.gromacs.org/index.php/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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