Re: firsttimestep

From: Jim Phillips (
Date: Tue Feb 24 2004 - 15:22:27 CST


I'm guessing this is NAMD 2.4 or 2.5b1 and you are using rigid bonds in
your simulation. The PRESSURE field is off during the first step due to
the SHAKE/RATTLE algorithm, but GPRESSURE is normal. This behavior should
be fixed in NAMD 2.5. The trajectory is unaffected in any case.


On Tue, 17 Feb 2004, Ekta Khurana wrote:

> Hi,
> I am continuing NAMD runs using restart files. I give the last step of
> previous run as the firsttimestep for the new run as mentioned in the
> tutorial.It does not write information to dcd files etc again for the
> firsttimestep of the new run but it does write the energies and pressure
> in the log file which are not the same as what it wrote for that time step
> in the previous run. The energies are very similar though but the new
> pressure is very high(around 7000 while it was in hundreds).It comes back
> to hundreds in the next step though. Why is NAMD doing that-should I just
> ignore these very high pressure values.I am using NVT ensemble.
> Thanks,
> Ekta
> --

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