I think your RMSD of 0.000539742 is quite a small value, which can be,
at least theoretically, caused by the accumulation of errors. Can you
simulate your protein for a longer time to show that RMSD is indeed
significant?
On Sat, Jul 28, 2012 at 1:01 AM,
wrote:
> Hi,
> my problem is, that duri
On 28/07/2012 3:01 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
my problem is, that during the md run the atoms are not frozen somehow.
During the minimization run everything worked out fine. But when I did a
md run the hydrogen atoms and the other atoms seems to be changes somehow
Hi,
my problem is, that during the md run the atoms are not frozen somehow.
During the minimization run everything worked out fine. But when I did a
md run the hydrogen atoms and the other atoms seems to be changes somehow.
I calculated the RMSD value and this is why I know that they change.
After
>
> I want to do a minimization and a md run with my protein. But I only want
> the hydrogen atoms to be minimized but not the rest of the protein.
> I use the
> freezegrps = Protein-H
> freezedim = Y Y Y
>
> option in my mdp files to make sure that they don't change.
>
> During the minimization st
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