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

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 12 17:44:51 CEST 2011

Anna Marabotti wrote:
> 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
> suggestions.
> 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
> prot_boxdodfull_rmsf.xvg
> 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
> prot_boxdodfull_rmsfchain.xvg
> but still the .xvg file appears with the data about the two chains
> superimposed.
> 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.

Why not?  This seems like the most obvious solution.  If you analyze both chains 
independently, isn't that what you're trying to achieve?

If you want to completely eliminate any reliance on chain identifiers or 
overlapping numbers, either (1) eliminate all chain IDs or (2) make them all the 
same, and then use genconf to renumber the whole coordinate file from 1.


> 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...
> Anna
> -----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
> 	system
> 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
> oscillates
>> 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
> value
>> itself; however, I would like to know if I use the correct reference file
> or
>> 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
> about
>> my question?
> If you've manipulated the trajectory with trjconv, then you need a
> corresponding 
> 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.
> -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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