[gmx-users] problem regarding pbc

sangeeta sangeeta at bic.boseinst.ernet.in
Wed Jan 24 09:30:21 CET 2007

Dear GROMACS list members,

   I have three questions,

   My protein has +2 charge, so I added two Cl atoms through the program 
genion and subsequently edited the  topol.top file, in spite of that while 
running mdrun it gave an error that  "FATAL error, CL atom type can not be 
found",I can not understand the problem.
   I wanted to include PBC in my simulation, I want to know that does 
Gromacs by default use the option by minimum image convention or we have to 
edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is 
being included in my simulation?
    In spite of having dssp and running it I can not get the .xpm files. 
Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx
are being produced.How can I generate those xpm files?  
    Waiting for your reply.


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