[gmx-users] size of the molecule

[Anton Feenstra]

raj vel wrote:

> hello all,
> i am unable to do mdrun, for a protein with 504
> aminoacids. while mdrun, LINCS warning and the
> pressure coupling is more than 1 amu and this aborts
> the mdrun. i was informed to increase tau_p, even that
> is not working. 
> but when i split the molecule (from PDB) into 100
> aminoacid each, mdrun runs properly. but the time
> taken by each fragment for mdrun differs very high.(
> 45 min for one segment and 48 hours for another
> segment).

You should carefully examine the parts of the protein that Lincs
complains about. My gues is that you will find (several) bad
contacts there, which you will have to get rid of. This you can
do 'manually' with a modeling program (or even with some versions
of rasmol) by moving the offending groups out of each others way.
Or you can do it by (repeated series of) position-restrained MD
and energy minimization, possibly without pressure coupling and
with a 1fs timestep in stead of 2fs.

> is that possible to do mdrun for a molecule with such
> high no. of amino acids??
> any suggestions

504 residues is not large, and, yes, Gromacs can handle that easily.
I run proteins of 450-500 residues regularly and as we speak there
is an mdrun running for GroEL/ES which has 14 subunits of ~400-500
residues each, and an additional 7 subunits of 200-300 residues.
(In total, there are >50000 atoms in the protein alone, and then
there is water around it as well!)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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