NAMD pressureProfile command

From: P.-L. Chau (
Date: Thu Jul 04 2013 - 16:52:00 CDT

I am trying to calculate the pressure profile using the NAMD command
pressureProfile and I have come across some difficulties. Could I ask for
some help and advice, please?

If I understand correctly, to calculate the pressure profile, one performs
a normal molecular dynamics run, and dumps the DCD file. One then takes
the *.conf file which has been used to generate the DCD, and adds a little
script to get it to calculate the pressure profile. One then runs NAMD
again using this modified *.conf file. This time, the programme only reads
the DCD and calculates pressure profile without running a simulation.

If this is correct, then I would like to report that, on the second pass
when NAMD reads the DCD file to calculate the pressure profile, I get a
lot of RATTLE errors.

I am quite confused, as RATTLE is associated with running molecular
dynamics, not with reading a DCD file. If NAMD is only reading a DCD file
on the second pass and not actually doing any simulations, why should
there by RATTLE errors?

I understand that you may need to read the actual files to see what is
happening. I shall be happy to show other NAMD users the exact files used
and the errors produced. But these files are large, so I shall only send
them on request.

Thank you very much indeed.

P-L Chau

Bioinformatique Structurale
Institut Pasteur
75724 Paris

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