[gmx-users] Re: g_mindist on rhombic dodecahedron system

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Jul 5 17:56:12 CEST 2011

Dear Tsjerk,
thank you very much for your answer. I completely re-analyzed my simulations
and I'm telling you all the problems I found.
First of all, please remember that this is a dimeric protein, formed by two
identical subunits, with no covalent interactions (no disulphide bridges and
so on).
Here the steps I used for the simulation.

pdb2gmx -f prot.pdb -o prot.gro -p prot.top

I used editconf to create the rhombic dodecahedric box and to center the
protein in the box. Here the exact string of commands:
editconf -f prot.gro -o prot_boxdod.gro -bt dodecahedron -d 1.5 -c
genbox -cp prot_boxdod.gro -cs -o prot_boxdodwat.gro -p prot.top
If I look at the prot_boxdodwat.gro file in VMD, I see a cubic box in which
the dimeric protein is in a corner (and with a little part of the protein
out of the box).
What's wrong with this command? Why I don't see a rhombic box? Why the
protein is not centered in the box? Why a part of the protein is outside the

grompp -f em.mdp -c prot_boxdodwat.gro -o prot_boxdodwat.tpr -p prot.top
trjconv -f prot_boxdodwat.gro -s prot_boxdodwat.tpr -pbc whole -ur compact
-o prot_boxdodwat_whole.gro
and looking at prot_boxdodwat_whole.gro with VMD I see exactly the same
thing as before. Why I cannot see a rhombic box?

I neutralized the system:
genion -s prot_boxdodwat.tpr -o prot_boxdodneu.gro -np 6 -pname NA -p
and used
grompp -f em.mdp -c prot_boxdodneu.gro -o prot_boxdodneu.tpr -p prot.top
trjconv -f prot_boxdodneu.gro -s prot_boxdodneu.tpr -pbc whole -ur compact
-o prot_boxdodneu_whole.gro
and looking at prot_boxdodneu_whole.gro with VMD I see exactly the same
thing: cubic box with dimeric protein in a corner (and a little part of the
protein out of box)

I minimized the system
mdrun -s prot_boxdodneu.tpr -deffnm prot_boxdodmin
(converged to Emtol < 500)
and obtained the system after minimization. 
Looking at prot_boxdodmin.gro file with VMD, now I see a rhombic box, but my
protein now is splitted into two monomers, one into the rhombic box (with a
little part outside) and the other monomer completely out of the box.
trjconv -f prot_boxdodmin.gro -s prot_boxdodneu.tpr -pbc whole -ur compact
-o prot_boxdodmin_whole.gro
and looking at the prot_boxdodmin_whole.gro file with VMD, nothing is

Continuing with NVT and NPT, nothing changes: always I see the protein
splitted into two monomers. Please remember that I NEVER see any error
message before/during/after calculations.

After the full MD, instead, I look at the prot_dodboxfull.gro file and I can
see the dimeric protein into the rhombic box (with a little part outside the
box), but the trajectory behaves as I told before: spikes for the first 10
ns and then nothing.
The reason why I obtained a <1 distance with g_mindist is probably due to
the reference I used, i.e. the .tpr file at the start of the simulation
(obtained from the npt trajectory, with the monomers splitted and one of
them outside the box).

I really didn't face a similar behaviour before, and I really don't know how
to cope with this protein. Any help will be appreciated.
Sorry for the length of the message, I tried to be as precise as possible.


Message: 4
Date: Tue, 5 Jul 2011 15:06:11 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] R: g_mindist on rhombic dodecahedron system
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
	<CABzE1Sg7n3EdyHLuTbJ=hWNdx0+1kr003E0gbuiC6RS78Nd6Pg at mail.gmail.com>
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Hi Anna,

The spikes going down to 0.1 nm can only be explained by a fragmented
representation of your protein in the frame. Mind that Gromacs does
not write molecules in one piece as it used to. You therefore have to
make all molecules whole prior to calling g_mindist. You mention doing
so, which raises the question what your actual command lines were, in
particular what you used as a reference structure. Or did you
accidentally use the original trajectory again, rather than the one
made whole? Please keep a record of the commands you used and paste
them in your mail so that we can better understand what may be
happening, rather than making (educated ;)) guesses.



On Tue, Jul 5, 2011 at 2:49 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> wrote:
> Dear users,
> can anybody give me suggestions about my questions below?
> Thank you very much
> Anna
> ________________________________
> Da: Anna Marabotti [mailto:anna.marabotti at isa.cnr.it]
> Inviato: lunedl 4 luglio 2011 17.43
> A: 'gmx-users at gromacs.org'
> Oggetto: g_mindist on rhombic dodecahedron system
> Dear users,
> following Tsjerk' suggestions, I simulate the protein which had some
> problems in periodic distance violations in a triclinic box, using instead
> rhombic dodecahedron box created with the options:
> editconf -f prot.gro -o prot_boxdod.gro -bt dodecahedron -d 1.5 -c
> Minimization, PR-NVT and PR-NPT went OK (no error messages, potential
> after minimization of about -1e+6). I run 30 ns full MD (no PR).
> At the end of the production MD, I would like to repeat the g_mindist
> analysis, so I can be sure my system does not suffer again of a periodic
> distance violation.
> I performed g_mindist on 4 different systems, and these are my results:
> 1) on the resulting trajectory: on average, the distance between two
> periodic distances calculated on the entire protein (option = 1) is > 3
> However, until 10 ns I can see several "spikes" going down to < 0.1 nm
> 2) on the resulting trajectory, applying trjconv -pbc nojump before
> g_mindist: on average, the distance is < 0.1 nm
> 3) on the resulting trajectory, applying trjconv -pbc whole -ur compact
> before g_mindist: the same as 1) (perfectly superimposable)
> 4) on the resulting trajectory, applying trjconv -pbc whole -ur compact,
> then trjconv -pbc nojump, before g_mindist calculation: the same as 2)
> (perfectly superimposable)
> My questions are:
> 1) do I have to transform in some (other) way the trajectory before
> calculating g_mindist? Do I have to calculate g_mindist in another way
> using a different group for calculations)?
> 2) given these results, can I consider this trajectory suitable for
> analysis? (maybe excluding the first 10 ns)
> 3) If not, what can I do more to have a suitable trajectory?
> Many thanks for any suggestions, I'm quite frustrating for not
> where the problem comes from...
> Anna
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "When a man with a gun meets a man with a pen, the man with the gun is a
> dead man"
> (Roberto Benigni, about Roberto Saviano)
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


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