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On 12/07/2011 4:46 AM, chicago.ecnu wrote:
<blockquote cite="mid:201107120246555931111@gmail.com" type="cite">
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<div>Dear Gromacs users,</div>
<div> </div>
<div> I'm want to use Gromacs as the main tool in my study ,
since Gromacs is much faster than other MD packages.</div>
<div> </div>
<div> I'm trying to switch from Amber to Gromacs recently.</div>
<div> </div>
<div> The system I test is a RNA , contains about 2000 atom.</div>
<div> </div>
<div> In tleap of Amber , the command is " solvateoct my_rna
TIP3PBOX 10" . Totally 40666 were added. </div>
<div> </div>
<div> In Gromacs, the command is </div>
<div style="text-indent: 2em;">"
<div>editconf -f nuc.gro -o nuc.box.gro -d 1.0 -bt octahedron -c</div>
<div>genbox -cp nuc.box.gro -cs spc216.gro -o k_solv.gro -p topol.top</div>
"</div>
<div> Totally 62799 waters were added. </div>
<div> </div>
<div> </div>
<div> Is there something wrong with the command I used ?</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
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