[gmx-users] Gromacs adds much more water than tleap in Amber when solvate ?

chicago.ecnu chicago.ecnu at gmail.com
Mon Jul 11 20:46:58 CEST 2011

Dear Gromacs users,

     I'm want to use Gromacs as the main tool in my study , since Gromacs is  much faster than other MD packages.

     I'm trying to switch from Amber to Gromacs recently.

     The system I test is a RNA , contains about 2000 atom.

     In tleap of Amber , the command is " solvateoct my_rna TIP3PBOX 10" .  Totally   40666 were added. 
     In Gromacs, the command is 
editconf -f nuc.gro -o nuc.box.gro  -d 1.0  -bt octahedron  -c
genbox -cp nuc.box.gro -cs spc216.gro -o k_solv.gro -p topol.top
      Totally 62799 waters were added. 

    Is there something wrong with the command I used ?

Many thanks for your help !

Chicago Ji
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