[gmx-users] kill some atoms

2008-09-14 Thread Vitaly Chaban 
Hi,

Is there a way in gromacs to kill some atoms.

For example, after the run one decreases the box volume using editconf
(or genbox). Evidently then some molecules appear to be outside the MD
box. The task is to kill those molecules.

Please give a hint.

-- 
Vitaly

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Re: [gmx-users] kill some atoms

2008-09-14 Thread Omer Markovitch 
What is the reason for shrinking the box?
If it is for technical reasons, for example - nicer visualization etc`, then
perhaps this could be done manually.
If you plan to use the smaller box later, then maybe you could do some part
of high pressure simulation, to reduce box size while keeping it physical.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] kill some atoms

2008-09-14 Thread Vitaly Chaban 
Omer,

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
manipulations.

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


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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