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

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 6 09:40:01 CET 2003

On Wed, 2003-11-05 at 17:43, Anton Feenstra wrote:
> 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...)

Another problem could be that your gro file is:


whereas your topology has

the order in the topology should match the gro file. grompp warns you
about atom-name mismatches  though

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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