[gmx-users] minimal distance between periodic images

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Dec 22 12:17:24 CET 2014

Hi Jinxin,

The distance should be at least half of the cut-off distance, such that the
total distance (twice the distance between protein and 'box edge') will be
larger than the cut-off distance. So you should be fine. Now, if the system
undergoes large conformational changes, that may still cause direct
interactions. However, the most common cause to find violations of the
minimum distance is that the molecule gets split over PBC. Make sure that
your protein is whole before running g_mindist.



On Mon, Dec 22, 2014 at 11:19 AM, jinxin <18819028611 at 163.com> wrote:
> Dear everyone,
>        During my simulation,  i set the option '-d 1.2' creates a buffer
> of 1.2 nm between the outside of the protein and the edge of the box.  In
> the mdp file, i set the rcoulomb=rvdw=1.4, cutoff-scheme = Verlet. After
> the simulation, i use g_mindist -pi to analyzed the minimal distance
> between periodic images , i found some values are less < 1.4. i think the
> promlem is that i should increase the value of '-d 1.2'. someone tell me
> that the value should twice the cut-off distance from the
> next nearest image of itself. however, i found some publication set the
> '-d 1.2', the coulomb and van der Waals cutoffs of 1.4 nm. please tell me ,
> if i set the set the rcoulomb=rvdw=1.4, which value of '-d ' should i set ?
> thank you every much!
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Tsjerk A. Wassenaar, Ph.D.

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