VMD-L Mailing List

From: Rita Cassia (Rita.Cassia_at_gmx.de)
Date: Fri Feb 23 2007 - 07:48:39 CST

Dear All,

after creating an ethanol box, using AMBER topology and coordinate files, I had used NAMD for a first simulation, starting at 0°K and in the configuration file, there are:
"dcd frequency = 50"
"run 2000"

Well, as other simulations, i could read the number of Frames in VMD, dividing the time of the simulation by the dcd frequency and added 1, from coordinate file. For example: a simulation with 8000000 ps and dcd frequency 40000, gave me 200 + 1 frames.

Well, now with ethanol, instead of having 41 frames, I got 43 frames...Besides that, in another simulation, heating from 100 K until 300 K, instead of having 120 frames, I have got 99, although the log files said that the NAMD calculations were done successfully.

I would be very glad if someone can help me to find out what's wrong.

Thanks in advance.

Rita Leite

Photobiophysik - Inst. für Physik
HU Berlin 

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