Re: Cannot specify both an initial temperature and a velocity file

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Thu May 04 2006 - 08:45:53 CDT

you need to comment out either line (binVelocities, set temperature).
when a temperature value is entered in the config, NAMD uses it to
generate a velocity for each atom -- following a Gaussian
distribution, together gives an instantaneous kinetic temperature of
the set value. you can not do both.

best,

marc
On May 4, 2006, at 7:44 AM, Osman Yogurtcu wrote:

> Hi,
>
>
> I am getting an error while continuing a NAMD run after the
> minimization, which says "Cannot specify both an initial
> temperature and a velocity file". Inside my .conf file I have these
> lines...
>
>
> structure ../common/1BFT_A_wb_ion.psf
>
> coordinates ../common/1BFT_A_wb_ion.pdb
>
> binCoordinates ../mini/res.coor
>
> binVelocities ../mini/res.vel
>
> extendedSystem ../mini/res.xsc
>
> set temperature 300
>
>
> The error suggests that I should comment out the temperature.
> However, my friends in the lab, although they have the exact code,
> do not receive any error. What am I missing? Is there something
> wrong with my minimization?
>
>
> Thanks
>
>
> Osman Yogurtcu
>

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