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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 12 05:21:22 CEST 2011

On 12/07/2011 4:46 AM, chicago.ecnu wrote:
> 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 ?

The two distances could mean all sorts of different things in the two 
codes. You'll need to check out the documentation of both. Additionally, 
the relative orientation of the octahedron and the solute can be relevant.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110712/4b6b6a98/attachment.html>

More information about the gromacs.org_gmx-users mailing list