From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 23 2007 - 09:05:15 CST

On 2/23/07, Rita Cassia <Rita.Cassia_at_gmx.de> wrote:

dear rita,

> 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.

this is next to impossible for somebody who has no psychic capabilities
or been standing next to you to see the exact sequence of what you did.

i suggest you examine your inputs and logfiles carefully again.

one - rather improbable - cause could be that your disk is full so that only
a part of the trajectory was written. another, that the .dcd file got corrupted
(check the VMD console for error messages). but most likely, you specified
something in your input that is different from what you think the
calculation did.

with the level of sophistication of current software, people tend to act as if
computers and software can read their minds. they can not.

cheers,
    axel.

>
> Thanks in advance.
>
> Rita Leite
>
> Photobiophysik - Inst. für Physik
> HU Berlin
>
>
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>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.