**From:** Jonathan Lee (*jonny5_at_rice.edu*)

**Date:** Tue Jun 19 2007 - 15:13:12 CDT

**Next message:**Sting: "Re: About pmf"**Previous message:**maria goranovic: "Changing loop to helix: restraining about 20 dihedral angles"**In reply to:**Jonathan Lee: "Re: Re: heat diffusion calculation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello all,

I've set up my system such that two ends of my rectangular box act as

my "shell" at 200K. I have periodic boundary conditions in all

directions. When I try the heat diffusion calculation from the tutorial

(with appropriate changes), I find that the temperature of my system

actually goes up. It reaches about 700-800K! I guess the langevin

dynamics help to control the system during minimization/equilibration

but are not present in the heat diffusion problem to control the

temperature. Can somebody help me troubleshoot this problem? Thanks.

Jonathan

p.s. I was having a problem during my minimization step where the

periodic cell was too small (even though I set it large enough to

contain the original configuration). I found one solution to this was

to turn on "useFlexibleCell" but is that ok?

Jonathan Lee wrote:

*> All,
*

*> Thanks everybody for your replies. I think I'm understanding it
*

*> better now. To follow up... I'm ultimately interested in calculating
*

*> the thermal conductivity in certain directions. For example, how well
*

*> heat will conduct in the z-direction versus in the x- or
*

*> y-directions. From my current understanding, the method outlined in
*

*> the tutorial would not work for something like this. It seems that
*

*> this method finds an isotropic diffusivity (and ultimately thermal
*

*> conductivity). Any clues on how I could approach this problem
*

*> (modifying the tutorial's method or otherwise)?
*

*>
*

*> On a side note, does anybody know how to apply periodic boundary
*

*> conditions in only one or two directions? Realistically, what type of
*

*> boundary conditions could I apply to the other direction(s)? If I
*

*> were to, say, heat one end of a rectangular prism domain and observe
*

*> the heat transfer down the length of the prism, surely I can't have
*

*> periodic boundary conditions in that direction.
*

*>
*

*> (By the way, Victor, it seems like we are in fact looking at
*

*> different versions of the tutorial. The temperature echoes appears at
*

*> the bottom of page 56 in my version.)
*

*>
*

*> Thanks,
*

*>
*

*> Jonathan
*

*>
*

*>
*

*> Victor Ovchinnikov wrote:
*

*>> Jonathan, The page numbers that you provide correspond to the
*

*>> calculations of the
*

*>> temperature echos from an MD simulation (at least in the tutorial
*

*>> version that I have)
*

*>>
*

*>> Nevertheless, I can try to answer some of your questions:
*

*>> 1) Yes, it is a boundary condition to the diffusion equation on page 47.
*

*>> 2) Not sure where you are; step 11 on p.55 deals with temperature echos;
*

*>> I'm certain that the script monitors the average temp of the system
*

*>> including the outer shell; this is an approximation, since analytically,
*

*>> the boundary has no volume, whereas in this case, it does; perhaps
*

*>> that's why the agreement with the theoretical plot on p.49 is not
*

*>> perfect.
*

*>>
*

*>> 3) The inner radius is 22, as defined in the VMD script that populates
*

*>> the beta column of the PDB; the simulation domain is a sphere with
*

*>> radius 26 Angstroms; so cutting off at 22 should apply to the outer
*

*>> layer of the water molecules, since the diameter of a water moelcule is
*

*>> roughly 3A. So the calculation _does_ take the radius into account; for
*

*>> a larger radius, you would have to first solvate & equilibrate the
*

*>> protein in a larger sphere; then when you ran VMD, increase to cutoff
*

*>> accordingly.
*

*>> 4) Yes, the problem is that you need an analytical formula for the
*

*>> solution of the heat equation in the rectangular domain; this should be
*

*>> obtainable from a PDE book as a series solution (just like the spherical
*

*>> formula) You would then need to take this solution and average over the
*

*>> size of the box -- i.e. integrate over x,y,z & divide by the box size;
*

*>> this would give you a an expression similar to the on p. 47
*

*>>
*

*>> Regarding the physics of measuring diffusion, you are correct; it is
*

*>> easiest to fix the temp. somewhere & put a probe at another location &
*

*>> record your temperature values; This is the lab experiment, which would
*

*>> give you a long-time averaged quantity (the duration of the experiment
*

*>> is of the order of seconds). However, you can only do MD for a few
*

*>> nanoseconds -- so your statistics for a quantity at one location would
*

*>> be extremely poor. What the method outlined in the tutorial says, is
*

*>> that you can still extract the diffusion coefficient from averaging over
*

*>> multiple regions -- in this case the entire domain (which will give you
*

*>> better statistics by orders of magnitude)
*

*>>
*

*>> Best, Victor
*

*>>
*

*>>
*

*>> On Mon, 2007-06-18 at 12:16 -0500, Jonathan Lee wrote:
*

*>>
*

*>>> Anybody? Thanks.
*

*>>>
*

*>>> Jonathan
*

*>>>
*

*>>>
*

*>>> Jonathan Lee wrote:
*

*>>>
*

*>>>> Hello all,
*

*>>>> I have some questions about the heat diffusion calculation in the
*

*>>>> NAMD tutorial (page 53).
*

*>>>>
*

*>>>> 1) The shell is maintained at a temperature of 200, right? (As
*

*>>>> opposed to just initialized to 200.)
*

*>>>> 2) What is the temperature that is output (step 11, page 55)? Is
*

*>>>> that the temperature of everything excluding the 200K shell?
*

*>>>> 3) It seems to me that the calculation should take into account the
*

*>>>> inner radius of the shell. If the radius is much larger, shouldn't
*

*>>>> it take a longer time for the diffusion to occur?
*

*>>>> 4) Can I do a similar calculation but with a rectangular prism
*

*>>>> domain (i.e. fix the temperature at one end and calculate the heat
*

*>>>> diffusion to the other end of the box)?
*

*>>>>
*

*>>>> Basically, my understanding is that the temperature should be
*

*>>>> maintained in one region and measured in another region a finite
*

*>>>> distance away. That distance (and the time of diffusion) should be
*

*>>>> taken into consideration when finding the diffusivity. Am I
*

*>>>> overlooking something? Thanks.
*

*>>>>
*

*>>>> Jonathan
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>
*

*>>
*

*>>
*

*>
*

*>
*

**Next message:**Sting: "Re: About pmf"**Previous message:**maria goranovic: "Changing loop to helix: restraining about 20 dihedral angles"**In reply to:**Jonathan Lee: "Re: Re: heat diffusion calculation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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