Re: [gmx-users] large error bars in PMF

2011-08-01 Thread Justin A. Lemkul
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

RE: [gmx-users] large error bars in PMF

2011-08-01 Thread Rebeca García Fandiño
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

RE: [gmx-users] large error bars in PMF

2011-07-22 Thread Rebeca García Fandiño
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 solvent around the protein is quite big, although I suppose that using a dodecahedron box for this system would hav

Re: [gmx-users] large error bars in PMF

2011-07-22 Thread Justin A. Lemkul
g 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] large error bars in PMF > >

RE: [gmx-users] large error bars in PMF

2011-07-22 Thread Rebeca García Fandiño
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

RE: [gmx-users] large error bars in PMF

2011-07-22 Thread Rebeca García Fandiño
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: g

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread XAvier Periole
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

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread Justin A. Lemkul
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

RE: [gmx-users] large error bars in PMF

2011-07-21 Thread Rebeca García Fandiño
? 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

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread XAvier Periole
-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 > > > > > > > > >

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread Justin A. Lemkul
but the 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.e

RE: [gmx-users] large error bars in PMF

2011-07-21 Thread Rebeca García Fandiño
lar box, but the 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...@v

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread Justin A. Lemkul
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-

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread Justin A. Lemkul
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-converged data". Oops, th

RE: [gmx-users] large error bars in PMF

2011-07-21 Thread Rebeca García Fandiño
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-converged data". Do you mean I will need also more windows

Re: [gmx-users] large error bars in PMF

2011-07-21 Thread Justin A. Lemkul
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