Hi Jagannath, You can convert the trajectory to a single PDB file with multiple models.
Cheers, Tsjerk On Mar 12, 2016 07:25, "jagannath mondal" <[email protected]> wrote: > Hi Tsjerk > Thanks for your suggestion on putting the parameters in bfactor column of > pdb. However, for this, the file format has to be a pdb format. However, if > I have a trajectory ( in xtc format) and each frame's 'bfactor' values are > getting updated, then do I need to convert entire xtc files into pdb files > for visualization? > Jagannath > > > On Tue, Mar 8, 2016 at 12:43 PM, Tsjerk Wassenaar <[email protected]> > wrote: > > > Hi Jagannath, > > > > Convert the file to PDB format and write the values to the b-factor > field. > > Most visualization programs can color by b-value. > > > > Cheers, > > > > Tsjerk > > On Mar 8, 2016 06:50, "Jagannath Mondal" <[email protected]> > wrote: > > > > > Dear gromacs-users > > > > > > I am sorry to write you a visualization-related query. I hope you can > > > help. > > > > > > My query is: How can I visualize a trajectory file ( example in vmd) > > where > > > I have an extra 4th column ( apart from x y z which are first 3 > columns) > > > which has a dynamically changing variable for each particles ? The plan > > is > > > to color gradient the atoms using the values of 4th column. > > > > > > > > > Is there a way to do it. I am sorry again to write you off the list. > > > Here is an excerpt from first few lines: > > > Jagannath > > > > > > 219GLN C 18 6.961000 4.468000 3.776000 1.678980 > > > > > > 220LEU C 37 6.753000 4.257000 3.980000 6.526284 > > > > > > 221THR C 51 6.618000 4.023000 4.151000 11.323132 > > > > > > 222ALA C 61 6.565000 3.742000 4.306000 26.957896 > > > > > > 223ALA C 71 6.409000 3.464000 4.313000 52.708403 > > > > > > 224GLN C 88 6.213000 3.540000 4.528000 > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
