Hi,
Actually you have already applied pbc,and there seems nothing wrong.
Some atoms are out of the box is common.
If your box vector is correct,then Gromacs will run successfuly afterwards.
At 2013-04-03 22:51:54,Abhinav Agrawal abhv.a...@gmail.com wrote:
Hi,
I have a polymer box on which I wish
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.
My em.mdp file is:
;
cpp = /usr/bin/cpp
define
On Wed, Apr 3, 2013 at 10:51 AM, Abhinav Agrawal abhv.a...@gmail.comwrote:
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not
There is no outside of the box.
Tsjerk
On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal abhv.a...@gmail.com wrote:
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess
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