[gmx-users] strange new H-H bond formation during MD

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 24 17:31:42 CEST 2006

Erik Marklund wrote:
> On Tue, 2006-10-24 at 04:59 +1000, Mark Abraham wrote:
>>Qiao Baofu wrote:
>>>Thanks.  Now I understand what happens.
>>>But in the user-manual of VMD, it is said that only four Gromacs file 
>>>(GRO, G96, XTC, TRR) and .pdb can be read by VMD. But only the .pdb 
>>>contain the information of bond-connectivity (if I understand 
>>>correctly). The point is that the output .pdb file from mdrun contains 
>>>only the coordinate information!  How can I tell VMD the 
>>>bond-connectivity information?!!
>>PDB files do not contain bond connectivity. By the look of 
>>http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html, you can't 
>>tell VMD your gromacs connectivity, unless you write your own plug-in to 
>>VMD (hint, hint). You could also try asking the VMD mailing list. Your 
>>simplest plan is likely to be to generate a PSF or PARM file with an 
>>equivalent topology, for they are used in other MD codes to contain the 
> That's not entirely true. Normally, pdb files do not contain topological
> information, but they CAN do so through a CONNECT block. This is
> probably why VMD claims that ".pdb contain the information of bond-
> connectivity" (don't use vmd myself, just cited Bafou above).

Well the URL I provided above omits PDB files from the list of file 
types that VMD reads for bond connectivity. Hence I suspect Baofu has 
misinterpreted something, or that manual section is incomplete.


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