[gmx-users] Using dummies in lipids

[Anton Feenstra]

Senthil Kandasamy wrote:
> Maybe Anton can help me with this one.
> 
> I want to use a dummy construction for POPE so that I can use a larger
> time step. Using united atoms for aliphatic hydrogens, the only explict
> hydrogens in the POPE are in the headgroup. It is basically an NH3- . So
> I used a dummy construction identical to that of a lysine.
[...]

It't been some time since I looked at the dummy parameter generation code,
so I'm not sure right away about how to fiz you problem. Given some time,
I'll try and look into this soon (remind me if you get impatient!).

Anyway, I'll try and give you some pointers. Do you have an .rtp entry for
POPE? Then you could try running it through 'pdb2gmx -dummy hydrogens'.
Otherwise, I've alsways put the 'dummy masses' (MNH3 type) next to the
NH3 group itselt. The grompp dummy parameter generation code may depend
on that. You can try and run 'grompp -debug' for lots of (useful?) info
in grompp.log, look for 'dummy atoms' (be warned that this slows down
grompp, and the logfile is pretty big!). Finally, you could check the code
in src/kernel/dum_parm.c yourself.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "This is Tense !" (Star Wars Episode I The Phantom    |
|             | Menace)                                               |
|_____________|_______________________________________________________|