[gmx-users] dppc's simulation

[David]

On Fri, 2003-02-21 at 06:05, kzong wrote:
> Dear all:
> I want to do some simulation about dppc bilayer, but I have some trouble. Because I build the initial structure with charmm, firstly I modify atom name according to the definition in dppc.itp(download from Dr.Tieleman's website) and convert pdb file to gro file by pdb2gmx, then I modify the example2.top(also from Dr.Tieleman's website) to fit my own system and write my own grompp.mdp file based the same file in gromacs benchmark package. When I run grompp and mdrun program, everything seems ok. But when I check the output coordinate file, I found that it's very different from the initial coordinate file even since only after 1 step. It seems that the coordinate file and topology file isn't consistent. But what's the matter? Have anything addition need to pay attention to?
> 
<
things may look very different when in fact it is only periodic boundary
conditions in action.(i.e. lipids moving ot the other side of the box)


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++