[gmx-users] Re: Questions

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 28 10:13:07 CEST 2009

Hi Lin,

I bounce this mail to the gromacs user list as the issues are well off
to be archived.

> I have two stupid questions here.

Well, that's up to us to decide ;)

> 1. I want to get the proper structure of lysozyme.
> From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL) and
> 2-hydroxethyl disulfide (HED) are removed.
> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
> Further, I remove the water, such as HOH, AHOH and BHOH.
> I don't know what is the differece between HOH, AHOH and BHOH.

The answer to this question is in the format specification of the PDB
file. The A and B are alternative identifiers and indicate that the
electron density can be explained by a water molecule that is
partially present at two sites. If you look at the occupancy field
you'll notice that the corresponding values are less than 1. In fact,
if you sum the occupancies for equivalent atoms in for A and B, they
will add up to 1.

> Then, I add all missing H atoms. => made the new pdb file => it is attached.
> Would you please take a look if the pdb file is corrct?

No, I'm not going to do that. Have a look at the structure to see if
it is okay and be sure to take into account whether you used a united
atom force field or an all atom one.

> In your tutorial, why don't you add the missing hydrogen atoms?

I do (or rather, I let the students do it ;)). It's one of the things
pdb2gmx does.

> Is it unnecessary to add the missing H atoms?

Each residue/molecule should have atoms (with coordinates) matching
with the description in the force field used. So if hydrogen atoms are
missing with respect to the force field, then they have to be added.

> HETATM 1504  O   HOH   445      36.056  19.096   6.798  1.00 34.30           O
> HETATM 1535  O  AHOH   482      24.352  20.291   2.379  0.50 20.49          O
> HETATM 1536  O  BHOH   482      24.181  18.429   1.588  0.50 24.50          O

> 2. Parallel computing in GROMACS
> What is the maximum number of computers in parallel computers in Gromacs?

There are people on the list better equipped to answer this question.
But you might be able to find a number of processors that will be
optimal for your case by readin the Gromacs 4 paper and doing some

> The more computers used in parallel, the less efficiency they have.

> For example, I want to see the micelle formation in 2 month and the parallel
> computing will be used.
> The starting configuration is random-spread of surfactants.
>  The  system is < = 0.25mM =>   300 solutes + so many water molecues (TIP3P water model)
>  What is your suggestion of the number of computers used in parallel
> computing?

I'm sorry, but I can't give an answer to this. If you have constructed
your system, you should probably just try different numbers of
processors for short (ps) simulations and from that determine what is
optimal for your case.

Hope it helps :)



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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