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" wrote:
>Hi,
>
>I have a polymer box on which I wish to apply energy
There is no outside of the box.
Tsjerk
On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal 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 this is because
On Wed, Apr 3, 2013 at 10:51 AM, Abhinav Agrawal 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 this is because periodic conditions are not applied.
>
> M
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
> defi
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