[gmx-users] kill some atoms

Vitaly Chaban chaban at univer.kharkov.ua
Sun Sep 14 11:12:11 CEST 2008


The situation is as follows. I simulate some pore (located at the
center of the box) and solvent is both inside and outside the pore. To
get a "right" density of solvent inside I make a system and let it
relax itself. Then I want to stop migrating solvent inside and
outside (inside an outside is intact!), so the easiest way is to reduce
one side of the box to be equal to the length of my pore (and re-center
the pore of course).

genbox and editconf can change the box parameters but they don't want
to kill the solvent which appears to be already not in the box after the

OM> What is the reason for shrinking the box?
OM> If it is for technical reasons, for example - nicer visualization etc`, then perhaps this could be done
OM> manually.

OM> If you plan to use the smaller box later, then maybe you could do some part of high pressure simulation,
OM>  to reduce box size while keeping it physical.

It seems that high pressure simulation reduces all side lengths (but I
need to reduce only the selected one). Am I wrong?


Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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