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