If you use periodic boundary conditions, there is no need that the
protein stays at one side of the box.
For the pulling simulation: Read the chapters 6.4 (explains the
pull-code) and 7.3.21 (explains the mdp-paramters).
Additional information you an also get from Justin Tutorial for Umbrella
Sa
Thank you all!
On Tue, Dec 11, 2012 at 12:54 PM, Leandro Bortot wrote:
> I have made SMD simulations in order to separate a Ca2+ ion from its
> complexation site in the protein, which had charge of about -6 e. Without
> position constraints in the protein alpha carbons it unfolded in every
I have made SMD simulations in order to separate a Ca2+ ion from its
complexation site in the protein, which had charge of about -6 e. Without
position constraints in the protein alpha carbons it unfolded in every
pull simulation.
2012/12/11 Thomas Schlesier
> wont happen, since the prob
I would also use the same residue from the pulling for the US.
One thing you should be aware of is the pulling dimension:
Now you have the pull-code only ativated for the z-direction. If you use
this still in the US the ion can move freely in the xy-plane (freely in
the sense of what is possible
Please keep all Gromacs-related correspondence on the gmx-users list.
Implicit solvent is available in the current 4.5 beta release.
Another tip: the mailing list search would have turned this same answer up in a
few seconds. This same question has been asked dozens of times.
-Justin
Samra
You really need pull_pbcatom0, since your slab is thicker than
half the box you otherwise can have periodicity errors.
Berk
> Date: Wed, 5 Aug 2009 15:27:06 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: pulling
>
m0).
Thx,
Alex
Berk Hess schrieb:
> No (completely) frozen groups are treated correctly.
> I had to look in (my own) code again, but for a fully frozen group
> the inverse mass is set to 0 in the pull code.
>
> Berk
>
> > Date: Fri, 31 Jul 2009 12:49:55 +0200
> > Fro
No (completely) frozen groups are treated correctly.
I had to look in (my own) code again, but for a fully frozen group
the inverse mass is set to 0 in the pull code.
Berk
> Date: Fri, 31 Jul 2009 12:49:55 +0200
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [g
Could it also be possible that 'pull = distance' makes problems because
it pulls both groups and here one group is frozen? Only an idea, i have
never tried to pull a frozen molecule.
Thomas
> --
>
> Message: 5
> Date: Fri, 31 Jul 2009 12:38:19 +0200
> From: Berk Hess
vector
between the two COM's.
Berk
> Date: Fri, 31 Jul 2009 09:58:56 +0200
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: Pulling a CG protein
>
> Hi Johnny,
> i replied something to the pull-code of your question. But problem was,
>
Hi Johnny,
i replied something to the pull-code of your question. But problem was,
i didn't edited the subject line...
So here is my answer (see below) with the right subject line (so that
you hopefully find it).
Hope it helps you.
Thomas
>
> Message: 3
> Date: Thu, 30 Jul 2009 12:08:40 -0700 (PD
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