[gmx-users] No velocities found

Xavier Periole x.periole at rug.nl
Mon Jun 13 12:16:07 CEST 2005

bmbbl at leeds.ac.uk wrote:

>Dear all,
>After the equilibrium simulation on the system, there were several molecules
>need to be removed from the conformation. So I convert .gro to .pdb and delete
>them from the .pdb file. And pasted the correponding velocities of the rest of
>atoms to then new .pdb file. However, when I tried to convert the new.pdb file
>back to .gro, editconf gives " No velocities found "
>What could the problem be?
There is no space for velocities in the pdb file. By converting a gro file
to pdb file you loose the velocities. Why don;t you just edit the gro file
and delete the molecules you want to delete. then change the number
of atom indicated at the beginning of the file and then use editconf to
clean up your file.


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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