[gmx-users] Protein split with mindist

[Tsjerk Wassenaar]

Hi Jinxin,

Better try trjconv -pbc whole
trjconv -pbc nojump should work if your protein is whole (and matching) in
the reference structure.
Fittings screws up the PBC.

Cheers,

Tsjerk
On Dec 23, 2014 6:02 AM, "jinxin" <18819028611 at 163.com> wrote:

> Hi Tsjerk    thank you very much ! as you said, the protein get splite and
> i can't get it back wiht command 'trjconv -pbc nojump -center'. however, i
> can use the command 'trjconv -fit rot+trans' to get the protein back. i
> don't know what the reason is. is my system broken?thank you very much!
> >
> >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.
> >
> >Cheers,
> >
> >Tsjerk
> >
> >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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