From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 08 2019 - 00:33:04 CDT

Hi,
  VMD presently only supports trajectories with a constant number of
particles. To accomodate a varying number of particles, you'd need to
create a number of "dummy" particles sufficient for the maximum particle
count for any frame in the trajectory, and mark the real vs. dummy particles
so that they can be easily disambiguated with simple atom selections.
Another option would be to load the varying particle counts into independent
VMD "molecules", and use the multiple molecule animation plugin to play
through them like a normal trajectory.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 01, 2019 at 08:44:18PM -0400, Lara rajam wrote:
> Dear VMD users,¬
> I have spliced water with my analysis for a peptide and wrote them as
> continuous pdb's, Now the issue is since the same peptide have¬ different
> number of water molecules in each frame I am not able to load as
> trajectory, Have anyone has comments to make this as trajectory.¬
> - Thanks in¬ advance

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/