Re: Re Re: heat diffusion

From: Jonathan Lee (jonny5_at_rice.edu)
Date: Mon Jun 25 2007 - 12:38:12 CDT

Hi Accomp,
I have tried it with and without the 2.5 margin (and the rest according
to your instructions). I'm also quite confident that my constrained
atoms are done correctly. In both cases (with and without 2.5 margin),
the minimization completes and almost immediately there is a the
following error:

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

What do you suggest? Thanks.

Jonathan

accomp lin wrote:
> Hi Jonathan
> I think you should try increase margin. Write margin 2.5 just below
> the line "#Input" .
> Turn the PME on ,and chose the PMEGridSize accordingly (page 23 of the
> tutorial). Also chose yes for useGroupPressure and no for
> useFlexibleCell and useConstantArea. Turn on the Minimization, do at
> least 2000 step of minimization.
> And the most important thing is to make sure you have altered the
> constrain atoms and tCouple parameter file "ubq_shell.pdb" to the
> proper one.
> hope it will work, and good luck!
> Accomp
>
> */Jonathan Lee <jonny5_at_rice.edu>/*
>
> Can anybody help me with this? Thanks.
>
> Jonathan
>
>
> Jonathan Lee wrote:
> > Hello all,
> > I am trying to do the heat diffusion computation from the tutorial
> > (section 2.2.1) but with some changes. Instead of a water sphere
> with
> > spherical boundary conditions, I would like to use a water box with
> > periodic boundary conditions (and cooled bath on two opposite
> ends).
> > I have been having problems where the temperature of the system
> rises
> > instead of falls (my bath temperature is 200K and initial system
> > temperature is 300K). I also sometimes get the error "Periodic
> box is
> > too small."
> > To begin, could somebody please confirm the changes that I should
> > make to the following file from the tutorial:
> >
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/2-6-heat-diff/ubq_cooling.conf
>
> >
> >
> > 1) Of course, change all the filenames and directories to the
> > appropriate ones
> > 2) Change the first line of the PBC to "if { 1 } {" and change the
> > values of the periodic cell appropriately
> > 3) Change the first line of the spherical BC to "if { 0 } {" or
> delete
> > altogether
> > 4) Should I turn on PME? I think it was causing problems for me,
> so I
> > left it off
> > 5) Should I turn on Constant Pressure Control?
> >
> > Also, what could possibly cause a system's temperature to rise
> > abnormally (it reaches 400-800K!)? Thanks.
> >
> > Jonathan
> >
> >
>
>
> ------------------------------------------------------------------------
> עŻ3.5G20M <http://cn.mail.yahoo.com>

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