Re: pressure profile

From: Grace Brannigan (
Date: Fri Dec 04 2009 - 10:04:46 CST

Hi Arturas,

You can run the non-bonded component on the fly - however, I usually find
that once I've run it I want to change the number of slabs or various other
parameters, so I usually end up running over the saved trajectory for
non-bonded as well. If you do run over the saved trajectory, be sure to set
the temperature in the conf file for *analysis* to something very low
(0.001K for instance). If it is set to 300 K for analysis NAMD will assign
random velocities for each frame, which will be added to the ideal gas
portion of the Virial and which will result in significant noise. As a
consequence of this noise, the ideal gas terms in P_zz may not cancel those
in P_xx and P_yy, and you will have a noisy contribution to your surface
tension that should not be there.

Hope this helps,


On Thu, Dec 3, 2009 at 5:22 PM, Ziemys, Arturas

> Hi,
> I ask some clarification about the Pressure Profile (PP) calculation.
> In order to get all the components of PP I must run PP calculation during
> (1) regular "on-line" MD job (kinetic,bonded,non-bonded parts), and (2) over
> saved trajectory (Ewald part). Is it right that full PP will be available
> just using this way ?
> Best
> Artuars
> -------------------------------------------
> Department of Nanomedicine and Biomedical Engineering (nBME)
> The University of Texas Health Science Center
> 1825 Pressler Street, Suite 537
> Houston, Texas, 77030
> Phone: (713) 500-2315
> Email :

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