[gmx-users] Problems for Equilibration with 256 DPPC obtained from 64 DPPC

[Anton Feenstra]

Yuhua Song wrote:

> Hi, 
> 
> With the 64DPPC.pdb bilayer download from Peter Tieleman's website, 
> using command: genconf -nbox 2 2 1, I generate the 256 DPPC bilayer,
> Looking from the vmd, it seems that everything is fine. But when I use
> NPT way to do the equilibration,it crashed, the following info is show
> during the run:, I try to change: tau_p, rlist, rcoulomb, rvdw, but
> nothing can help. Could you please help me to take 
> a look.  

I would guess you have 'divided' some of your molecules across the
periodic boundaries, or rather, that is the way they already were in
the initial pdb file (from Peter's website). Then, when you 'multiply'
your systen using genconf, some lipids on the boundary will actually
be built from parts of different molecules (as defined in the topology),
and parts of one molecule will be in different locations in your box.

A solution could be to e.g. energy minimize Peter's pdb file first.
The minimization itself is not necessary, but as a side-effect, mdrun
will write the coordinates with all molecules 'whole'. That conformation
should be safe to multiply in genconf and used as starting point for
a simulation. (Perhaps there is a tool to do that, other than mdrun,
that may be easier, but none that I can think of now...)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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