Dear Justin, Actually, I used -d option because you said the atoms in the box must be half a bond length from the edges of box...I thought maybe this can be done by -d...
With PRODRG I am unable to produce coordinate file a chain with less than three C atoms. I sketched the molecules: C-C ethane C=C Ethylene but I am getting a message: ERRDRG> PRODRG does not deal with mono/di-atomic molecules. PRODRG> Program terminated unsuccessfully, sorry! 1- Could you please help me with this. (actually I need structure file of ethylene in the future) 2- How can I generate structure file of repeating unit -CH2-CH2- with PRODRG. I tried the followings...and all I am getting is the above message.. :( H H | | C-C | | H H H H | | -C-C- | | H H -C-C- Moeed
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
