For example, I have production1.dcd, production2.dcd, and go on. As a second question which structure will be valuable for me as reference? Let's say I have two files as wat_ion.psf and wat_ion.pdb. I have carried out 1000 steps minimization and 1 ns equilibrium simulation by using these structures. After that, I have carried out 2 production simulations (pro...1.dcd and pro...2.dcd) by 1 ns. I want to see the RMSD curve for the whole 2-ns-production simulation. However, I want the first frame of this simulation to be my reference.
Thank you very much in advance.
Aw, OK. Anyway, maybe you can try the rmsd_matrix script here: http://www.ks.uiuc.edu/Research/vmd/script_library/
And as for the input loading process you can use something similar to this:
set liposom [mol new cg_DLPE_32nm.psf type psf waitfor all]
mol addfile DLPE-32nm-npt-1.dcd type dcd first 0 last -1 waitfor all molid $liposom
mol addfile DLPE-32nm-npt-2.dcd type dcd first 0 last -1 waitfor all molid $liposom
Change the psf and dcd file name according to yours.
First of all, open the PSF file, then load the 1st and 2nd trajectory to the PSF file. Then you can calculate the RMSD using the RMSD Trajectory Tool via Extensions > Analysis > RMSD Trajectory Tool. A new window will appear, then you have to type the atom selection inside the top left text-box (the default is protein), if you would like to calculate the whole system then type all in the box. Also notice that by default the noh is checked, means that by default the displacement of hydrogen atom is not taken into account.
As for the frame ref, since you would like to use the first frame then let the default be, since 0 (zero) is the first frame. Then check the time and plot tick box like in the picture below. Then click the RMSD button, and the RMSD Trajectory plot will appear.
Aw, OK. Anyway, maybe you can try the rmsd_matrix script here: http://www.ks.uiuc.edu/Research/vmd/script_library/
And as for the input loading process you can use something similar to this:
set liposom [mol new cg_DLPE_32nm.psf type psf waitfor all]
mol addfile DLPE-32nm-npt-1.dcd type dcd first 0 last -1 waitfor all molid $liposom
mol addfile DLPE-32nm-npt-2.dcd type dcd first 0 last -1 waitfor all molid $liposom
Change the psf and dcd file name according to yours.
An analysis package that has been invaluable to my work in MD is ProDy:
http://prody.csb.pitt.edu/
It includes some very powerful tools for working with, modifying and analyzing trajectory files.
Just thought I would mention it.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics