VMD-L Mailing List

From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Mon Mar 27 2006 - 09:16:54 CST

Hi

2 problems here, at least!

1 - If VMD reports the error of "wrong number of atoms", that's what it is ;-) You are feeding VMD with a topology/coordinate file with a different number of atoms with respect to the trajectory .xtc/.trr. Probably your top/coordinate file has only the protein atoms (since the problem seems to disappear deleting the solvent molecules).

2 - If you are getting strange things when visualizing the traj on VMD, that's because the protein in not whole, or is some king of wrap error, or atom sorting problem. You have some tools on gmx pack to take care of those issues (trjconv ?). The gmx viewer gives you the expected thing, because it takes care of the trajectory before loading it (not sure about this).

Best
Nuno

  ----- Original Message -----
  From: hayagreevan R
  To: vmd-l_at_ks.uiuc.edu
  Sent: Monday, March 27, 2006 12:30 PM
  Subject: vmd-l: problem with viewing gromacs xtc files in vmd

  hi all,
  i am doing my gromacs simulations in cluster and viewing it in vmd in my local system.
  I can view my output in gromacs trajectory viewer.But i am unable to view it in vmd.Initially vmd showed error of wrong number of atoms.So i had to remove all water molecules from my protein.But now,it is not showing any error but the output is undecipherable.It is just a combination of lines.The wierdest part being,the trajectory still runs even in these lines.
  I switched back to gromacs trajectory viewer to check if the error was in vmd or in gromacs.It again had no problem in gromacs.
  I donno where the problem is ?
  If anybody had experienced this problem beforehand,please help me with the solution for it.
  cheers
  hayagreevan

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