[gmx-users] smd

[Erik Marklund]

Hi,

I may be wrong, but the phrase "center of the box" suggests that what you see is just a visualisation artefact. What does the pulling distance over time tell you? Is it longer than half the box size?

Kind regards,
Erik

On 7 Nov 2014, at 13:52, Victor Rosas Garcia <rosas.victor at gmail.com> wrote:

> That is the first thing I would do: make the box larger, so the total
> pulling distance is less than half the box length.
> 
> regards
> 
> Victor
> 
> 2014-11-06 23:40 GMT-06:00 Yixin Ai <aixintiankong at 126.com>:
>> Dear everyone，
>>    i want to use gromacs to perform the steered molecular dynamcs simulation. My system is the protein-ligand complex in the center of the box an i want to pull out of the ligand form the protein ative site.  i have set the pbc in my mdp file.  However,  after simulation, i find that the ligand out of the box and get into the next unit cell. How does this make sense? should i the box larger to keep the liand in the original unit cell?
>> 
>> 
>> 
>> 
>> 
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