VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Tue May 11 2010 - 07:26:58 CDT

Hi Sarah,

It is probably better to run namd from the command line and define your own configuration file since this will give you more control over what is going on.

First there is no relationship between the length of a simulation (how long it takes to run) and the number of frames. You could have a simulation that runs 500 steps and one that runs 50000 steps and both output 100 frames (the first write a frame every 5 steps, the second write a frame every 500 steps). Given the same system and simulation parameters, you would expect the later to take about 100 times longer. There is actual timing information in the log file.

As far as your problem with VMD displaying the results from the trajectory, it is difficult to diagnose what is going on without having the actual error message. When you say that VMD opens the files, do you actually see that it has loaded a molecule with the correct number of atoms and frames in the main VMD window? Are you able to open and display the solvated system? Make sure that the dcd file that you are trying to load has the same number of atoms as the psf file (i.e. don't load the dcd file from the simulation without water into the psf file of the system with water).

Sorry I couldn't be of more help. If you provide more information in a concise and clear way, myself or someone else from the mailing list should be able to provide you with further assistance.

Josh

On May 11, 2010, at 3:29 AM, sarah k wrote:

>
> dear all,
>
> i ran a complex immersed in water box using gui. i first tried 5000 minimization and 5000000 MD steps. it resulted a fast simulation in 100 frames! then, i used 5000 minimization and 170000000 MD steps. again it was simulated in 100 frames so faster than i expected.
> I'm sure that there is a problem. I've tried some other complexes, protein+ ligands) the lasted much longer time and more frames.
> i also tried other minimization step numbers. it just runs minimization. i removed the water box and did the simulation again. this time MD was done too but when i open *.dcd file into *.psf file VMD opens them but doesn't display anything and when i want to plot RMSD it face error stating it can't work with floating numbers. I've checked my *.log file. it was perfect.
>
> it's very important in my research to run simulation in water box or sphere. how can i fix all these problems?
>
>
> Enjoy life,
> Sarah K.
>