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

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Jul 12 15:44:52 CEST 2011

I hope this will be the last message on this subject...sorry to bother you,
but I'd need another hint about analysis.
All OK about the new reference file that I created following Justin's
The problem now is that my protein is a homodimeric protein, and when I do:
g_rmsf -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_0ns_fix.gro -o

the .xvg file comes with the analyses of both subunits superimposed. I tried
to avoid this first creating a .pdb file from the
prot_boxdodfull_0ns_fix.gro file:
editconf -f prot_boxdodfull_0ns_fix.gro -s prot_boxdodfull_0ns_fix.pdb

then adding the chain identifiers "A" and "B" to my .pdb file (I simply
edited it), and finally I used
g_rmsf -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_0ns_fix_chain.pdb -o

but still the .xvg file appears with the data about the two chains
I also tried to create an .ndx file, in which I created two groups (chA and
chB), but it seems to me that they are not suitable for my need.

Do you have any hints about? FYI, I'm currently using Gromacs 4.5.4, and
therefore the residues of the proteins were not renumbered.

Thank you for your infinite patience...

-----Messaggio originale-----
Date: Mon, 11 Jul 2011 10:29:51 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] R: Re: g_mindist on rhombic dodecahedron
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4E1B08DF.1060401 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear Justin, dear all,
> following your suggestion I used the command:
> trjconv -f prot_boxdodfull.xtc -s prot_boxdodfull.tpr -pbc mol -ur compact
> -o prot_boxdodfull_mol.xtc
> to convert my simulations, and as you anticipated all went OK: now my
> trajectories are without spikes, the protein is entirely in the rhombic
> dodecahedric box and the minimum distance is never lower than 2.5 nm, so I
> think that the simulations went properly.
> Now I have another doubt. In order to analyze my data (e.g. with g_rmsf,
> g_rms etc), which is the more correct reference file? Usually I use as
> reference file the .tpr input file of the full MD trajectory. I used this
> file also this time with the command:
> g_rms -f prot_boxdodfull_mol.xtc -s prot_boxdodfull.tpr -o
> prot_boxdodfull_rms.xvg
> Apparently, there are no main irregular behaviours (the RMS value
> between 4.2 and 4.25 nm, so I think I can assume it is quite stable). The
> absolute value of RMS is however very high with respect to the ones I used
> to see (that are generally lower than 1 nm). I assume that the important
> thing in this kind of analysis is the variation of the value, not the
> itself; however, I would like to know if I use the correct reference file
> if I have to create another reference file in which I "trjconv'ed" (how?)
> also the reference structure. Could you please give me some suggestion
> my question?

If you've manipulated the trajectory with trjconv, then you need a
reference frame for position-dependent quantities.  For RMSD, RMSF, etc I 
usually do something like:

editconf -f start.tpr -o 0ns.gro
trjconv -s start.tpr -f 0ns.gro -pbc mol -ur compact -o 0ns_fix.gro
g_rms -s 0ns_fix.gro -f traj_fix.xtc

Other manipulations may be necessary if the protein is a dimer, etc.


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