Re: [gmx-users] boundaries in PMF

2012-05-31 Thread Justin A. Lemkul
13:45:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] boundaries in PMF > > > > On 5/31/12 1:38 PM, Rebeca García Fandiño wrote: > > Thanks a lot for your quick answer. > > The mdp file I have used is copied below. Wh

RE: [gmx-users] boundaries in PMF

2012-05-31 Thread Rebeca García Fandiño
your help. Best wishes, Rebeca. > Date: Thu, 31 May 2012 13:45:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] boundaries in PMF > > > > On 5/31/12 1:38 PM, Rebeca García Fandiño wrote: > > Thanks a lot for your quick answer. &

Re: [gmx-users] boundaries in PMF

2012-05-31 Thread Justin A. Lemkul
: Thu, 31 May 2012 13:25:26 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] boundaries in PMF > > > > On 5/31/12 1:20 PM, Rebeca García Fandiño wrote: > > Hi, > > I am trying to calculate a PMF for an ion along a channel

RE: [gmx-users] boundaries in PMF

2012-05-31 Thread Rebeca García Fandiño
l^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps > Date: Thu, 31 May 2012 13:25:26 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] boundaries in PMF > > > > On 5/31/12 1:20 PM, Rebeca G

Re: [gmx-users] boundaries in PMF

2012-05-31 Thread Justin A. Lemkul
On 5/31/12 1:20 PM, Rebeca García Fandiño wrote: Hi, I am trying to calculate a PMF for an ion along a channel. Everything went OK, but when I used g_wham I got a profile with strange dimensions for the x-axis. What are the boundaries g_wham is using for calculating the units of x-axis? The