[gmx-users] about periodic image minimum distance

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Sep 20 12:34:27 CEST 2011

Dear gmx-users,
I'm doing several simulations of a monomeric protein with different ligands.
I had several frustrating experiences because I found that at the end of
simulations, I found that my complexes violate the minimum periodic image
I'm using Gromacs 4.5.3 and for all my simulations I set a triclinic box
with the command:
editconf -f prot.gro -o prot_box.gro -bt triclinic -d 1.5 -c
I think that this dimension is sufficient since I'm using rcoul= 1.0 and
rvdw=1.4 nm. I'm currently using amber99sb force field with tip3p water; the
system was neutralized with Na.
I have minimized (to Emtol=500) my system, equilibrated with 20 psec NVT+100
ps NPT (I checked the energies, and they were all constant), then submitted
to a full MD for 30 ns.
When I had a look at the trajectory using VMD, I saw that the protein goes
partially out of the box, therefore I used:
trjconv -f prot_full.xtc -s prot_full.tpr -o prot_fullC.xtc -pbc nojump
(selection: System=0)
and I analysed the new trajectory with:
g_mindist -f prot_fullC.xtc -s prot_full.tpr -od prot_fullC_mindist.xvg -pi
(selection: Protein=1)
The graph shows that the minimum periodic image is < 1.4 nm for a large part
of the trajectories (and even < 1.0 nm in some cases), therefore I'm
assuming that the protein interacts with its periodic images (and that the
trajectories must be thrown away...)
I would like to ask some questions. Maybe they are trivial, but I hope the
answers will be useful not for me only.
1) Am I doing correctly the analyses? Am I indicating correctly the System
(option 0) to perform the nojump option, and the Protein (option 1) to
analyse the minimum distance?
2) What could be the causes for these recurrent periodic image violations in
my system(s)? Why does a protein "go out" of the box? Can I argue that the
box is too small? Can I argue that the system is not fully relaxed before
the production MD?  What are the analyses that I can make to assess these
conditions before doing the MD? 
3) What are the solutions? Do I have to increase the box dimensions? Do I
have to change the box type? In another case, I solved the problem using a
rhombic dodecahedron box, so is this a problem recurrent only for triclinic
box, or not? Can a longer stabilization of the system avoid this problem? 
In summary, I'd like to know if there is a way to predict the risk of having
a similar problem looking at the system BEFORE simulation is made (and time
is wasted...), and if it depends on some incorrect setting of the system
(maybe some .mpd option?), or not.
Thank you very much for your answers.
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabotti at isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with a gun is a dead
(Roberto Benigni, about Roberto Saviano)
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