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Bug #18

Implement position rescaling with Rahman Parrinello barostat.

Added by Ramon Garcia about 14 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
Low
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Althougth there is some ongoing work to enhance the barostat with Gromacs, the
current barostat can be made more accurate with a painless change. In
do_update_md, modify the updating of the coordinates to include the change of
the box. In fact, I believe that not doing so was a misunderstanding of the
equations. The differential equation of the coordinates, in the box reference
frame is:

m_i d^2s_i/dt^2 = h^(-1) f_i - m_i G^(-1) dG/dt d s_i/dt

s = coordinates in the box frame
h = box matrix, transposed of Gromacs box
G = h^t t

Looking at Gromacs code in do_update_md and parrinellorahman_pcoupl and
comparing to the equation above we see that the velocity is defined as:

v_i = h ds_i/dt

therefore, the updating of the coordinates should be

dx_i/dt = d(h s_i)/dt = dh/dt * s_i + h * d s_i/dt = = dh/dt * h^(-1) * x_i + v_i = = M * x_i + v_i

(the last step assumes that dh/dt * h^(-1) is symmetric)

patch_update (2 KB) patch_update Patch to implement the feature described. Ramon Garcia, 10/10/2005 05:29 PM
patch_update (1.98 KB) patch_update Small correction to the previous patch. Ramon Garcia, 10/10/2005 07:16 PM

History

#1 Updated by Ramon Garcia about 14 years ago

Created an attachment (id=3)
Patch to implement the feature described.

Do patch < the_patch in the directory of update.c

#2 Updated by Ramon Garcia about 14 years ago

Created an attachment (id=4)
Small correction to the previous patch.

#3 Updated by Erik Lindahl about 14 years ago

Hi Ramon,

Thanks - we'll look into this later. We just have to stabilize 3.3 first, and then get back to working in the
head branch (where this will go).

#4 Updated by David van der Spoel over 12 years ago

This bug goes the same fate as 14 but its contents have been copied to the wiki.

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