[gmx-users] dppc's simulation

David spoel at xray.bmc.uu.se
Fri Feb 21 06:54:23 CET 2003

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

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