[gmx-users] Re: Questions

[David van der Spoel]

Chih-Ying Lin wrote:
> Hi Tsjerk:
> I still have questions here.
> 
> 1. Although you have explained the differece between HOH, AHOH and
> BHOH, I do not fully understand.     => Can I delete all of atoms,
> HOH, AHOH and BHOH ?
> 
> 2. So, in your tutorial, you use "united atom" algorithm, right?
> and, "pdb2gmx" can recognize the "united atoms" and give them the
> proper force fields, right?
> 
> 
> 3. If one want to use the "all-atom algorithm", use the command
> "protonate + protein pdb file"  first to add all missing hydrogens,
> then, use "pdb2gmx" to get an all-atom force field parameters, right?
No. just pdb2gmx -ff oplsaa
> 
> 4. In your last email => where did you get the following information?
> => I re-check the original 1LW9.pdb => I did not get the information by myself.
> 
> "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."
> 
> 
> 
> Thank you very much,
> Lin
> 
> 
> 
> 
> On 4/28/09, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>> 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
>>  tests.
>>
>>
>>  > 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 :)
>>
>>  Cheers,
>>
>>  Tsjerk
>>
>>  --
>>  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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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se