[gmx-users] minimal distance between periodic images

jinxin 18819028611 at 163.com
Mon Dec 22 11:20:03 CET 2014

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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