; To:gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
>
>
>
> On 5/31/12 3:37 PM, Rebeca Garc?a Fandi?o wrote:
> > Hi,
> > the center of mass of my channel is at the middle of the ion channel, and
it is
> > a symmetric system, so I sup
.@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
>
>
>
> On 5/31/12 3:37 PM, Rebeca García Fandiño wrote:
> > Hi,
> > the center of mass of my channel is at the middle of the ion channel, and
> > it is
> > a symmetric sy
Thu, 31 May 2012 15:52:48 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
>
>
>
> On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:
> > OK,
> > however, just one point about your last comment:
> >
> &
On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:
OK,
however, just one point about your last comment:
> I suspect this is why g_wham is finding a range of values only equal to half
of
> your expected reaction coordinate; it is considering only the positive
> displacement along the reaction
reaction coordinate.
-Justin
Thanks a lot for all your comments!!
Best wishes,
Rebeca.
> Date: Thu, 31 May 2012 20:08:26 +0200
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: boundaries in PMF
>
> Where is the center of mass of reference
; From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: boundaries in PMF
>
> Where is the center of mass of reference group (MOL) located?
>
> It seems that the COM is near the middle of the ion channel. Since you
> use 'pull_geometry=dist
Where is the center of mass of reference group (MOL) located?
It seems that the COM is near the middle of the ion channel. Since you
use 'pull_geometry=distance', g_wham will look only for the distance
between 'MOL' and 'Na' and that leads to problem.
If the com of 'MOL' sits in the center of t
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