Thanks! Your suggestion 3 solves the problem! On Wed, Aug 1, 2012 at 2:25 PM, Christopher Neale <[email protected]> wrote: > 1. does topol.tpr really correspond to traj.xtc? You don't need to specify -s > to simply use the -b and -e options > to trjconv so simply eliminate that.
Yes. topol.tpr matches traj.xtc. But indeed trjconv shouldn't need the structure file and removing -s topol.tpr option eliminates the problem. > 2. is there a file called index.ndx in that directory? That is the default > name of the index file for trjconv input > and make_ndx output, so perhaps trjconv is picking up an index file that is > not appropriate for this system. Usually no. Even in the case that there is such index file, index.ndx matches the system being analyzed. > 3. You say that only a portion of the atoms have been written to the .xtc. Do > you mean that you did that straight > out of mdrun? Your trjconv should then work fine if you simply don't give it > the .tpr file. To do analysis, you will > need to create a new .tpr file that has atoms corresponding to the ones that > you wrote out. If, for example, you > did not write out the coordinates of one protein molecule, then make a new > .top and .gro file corresponding to > that system and run them through grompp to get a new .tpr file. You can use > this .tpr file for your analysis (but not > for simulations of the entire system). Yes. I set xtc-grps to contain only part of the system in grompp.mdp before generating the topol.tpr input file. Generating a new tpr file will indeed make the analysis tool happy. Thanks!! --------------- However, I think the analysis tools can be made a little more convenient, since generating a new tpr file means that all conf.gro, grompp.mdp, and topol.top have to be changed accordingly. This will be a lot of (meaningless) work -- or am I missing some easier approach again? Thanks, Roc > Chris. > > -- original message -- > > I tried to use "g_msd -s topol.tpr -f traj.xtc -o msd.xvg -trestart > 500" to calculate the mean-squared displacements. But the results are > clearly erroneous: the first 2500 entries in the output are all > "-nan", and after that values stat constant (including zeros). I > suspected that this may be related to that I have too many frames > (20001) and too long simulation length (20 ns), so I tried to reduce > them with the command "trjconv -f traj.xtc -s topol.tpr -b 0 -e 1000 > -o traj.1ns.xtc" to split the trajectory file, but trjconv exited with > an error like "Index[0] 1234 is larger than the number of atoms in the > trajectory file (12). There is a mismatch in the contents of your -f, > -s and/or -n files." > > Now I think both problems may be due to the fact that only a portion > of all the atoms in the system have been written to the trajectory, > and other atoms are kept fixed. But I am fairly new to Gromacs, and > I'm wondering if I have missed anything. > > Thanks, > > Roc > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
