[gmx-users] dppc's simulation

kzong kzong at 263.sina.com
Fri Feb 21 06:05:08 CET 2003

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?


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