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. 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" <[email protected]> Subject: Re: [gmx-users] R: Re: g_mindist on rhombic dodecahedron system To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
