gmx-users@gromacs.org
Subject: RE: [gmx-users] large error bars in PMF
Date: Fri, 22 Jul 2011 12:41:34 +
I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total
pulling was 5nm along the z direction. I dont´t think there could be a
problem with the PBC, since the layer of solven
w should analyze the results obtaind from "pull_dim = Y Y Y" ?
Thanks a lot for your help.
Best wishes,
Rebeca.
From: rega...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] large error bars in PMF
Date: Fri, 22 Jul 2011 12:41:34 +
I have used a cubic box of dime
have been better.
I will try now the "pull_dim = Y Y Y" and see what it happens.
Thanks a lot for the suggestions!
Best wishes,
Rebeca.
> Date: Fri, 22 Jul 2011 08:23:18 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] large error bars
I see now what you mean. As it happens, I doubt that this would have
caused the problem since no force was applied on X and Y dimensions,
so it would require that there was a PBC-based distance degeneracy
along Z, although this is of course possible and hopefully Rebecca
will answer this pa
box is going to avoid this.
Would it be better a truncated octahedron?
Thanks a lot for your help.
Best wishes,
Rebeca.
[Hide Quoted Text]
Date: Thu, 21 Jul 2011 15:16:52 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: FW: [gmx-users] large error bars in PMF
Rebeca Gar
5:16:52 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: FW: [gmx-users] large error bars in PMF
Rebeca García Fandiño wrote:
I am trying to achieve the binding energy of the dimer composed by the
two small cyclic peptides, to compare it with experimental. What
advantages wou
Forget my last mail, I was not seeing the box correctly.
Sorry about that.
Best wishes,
Rebeca.
From: rega...@hotmail.com
To: jalem...@vt.edu; gmx-users@gromacs.org
Subject: RE: [gmx-users] large error bars in PMF
Date: Fri, 22 Jul 2011 10:15:27 +
CC:
Hi again,
I have one doub about
.
Best wishes,
Rebeca.
> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am trying to achieve the b
default? How could I calculate the errors based on the PMFs
aligned on the long distance value?
Thanks a lot for all the help.
Best wishes,
Rebeca.
> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> Date: Thu, 21 Jul 2011 14
continuous PMF). You can set whichever value of the reaction
coordinate you want to take as zero with the -zprof0 option.
-Justin
Thanks a lot for all the help.
Best wishes,
Rebeca.
> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error ba
? How could I calculate the errors based on the PMFs aligned on the long
distance value?
Thanks a lot for all the help.
Best wishes,
Rebeca.
> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> Date: Thu, 21 Jul 2011 14
-Justin
>
> > Thanks a lot!
> > Rebeca.
> >
> > > Date: Thu, 21 Jul 2011 14:14:44 -0400
> > > From: jalem...@vt.edu
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] large error bars in PMF
> > >
> > >
> > >
ain for your help.
Best wishes,
Rebeca.
> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am tr
a lot again for your help.
Best wishes,
Rebeca.
> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am t
e peptides are not playing nice. I feel like this
discussion has come up at least once or twice before, though...
-Justin
Thanks a lot!
Rebeca.
> Date: Thu, 21 Jul 2011 14:14:44 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] l
jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> > Hi,
> > thanks a lot for your quick answer.
> > What I am trying to pull are two small peptides one from another (r_1
> &
Justin A. Lemkul wrote:
Rebeca García Fandiño wrote:
Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1
and r_2).
I did not understand very well your last suggestion: "...if you want
reasonable error bars you will not lots of well-
--
From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Thu, 21 Jul 2011 16:36:59 +0000
Subject: [gmx-users] large error bars in PMF
Hi,
I am trying to calculate the binding energy of two molecules using the
PMF (Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have wr
help.
Best wishes,
Rebeca.
From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Thu, 21 Jul 2011 16:36:59 +
Subject: [gmx-users] large error bars in PMF
Hi,
I am trying to calculate the binding energy of two molecules using the PMF
(Umbrella Sampling method) and Gromacs 4.0.
Rebeca García Fandiño wrote:
Hi,
I am trying to calculate the binding energy of two molecules using the
PMF (Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of
windows used in the Umbrella Sampling calculations different result
Hi,
I am trying to calculate the binding energy of two molecules using the PMF
(Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of
windows used in the Umbrella Sampling calculations different results were
obtained, and I was
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