Re: [gmx-users] umbrella sampling (PMF) position discrepancy

insights, Raphael On Tue, Sep 11, 2012 at 5:22 PM, Raphael Alhadeff < raphael.alhad...@mail.huji.ac.il> wrote: > Thank you all for your help, > > Sheeba- > Yes, I get both positive and negative results. I think what you describe > is what I would get if I used 'distan

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

Thank you all for your help, Sheeba- Yes, I get both positive and negative results. I think what you describe is what I would get if I used 'distance' for the geometry. In any case, I have values from +2 to about -3, and they are not evenly distributed (unlike the coordinates, which are more or le

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

Hi Justin, thank you for you quick reply. On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote: > > > On 9/10/12 11:22 AM, Raphael Alhadeff wrote: > >> Dear Gromacs users, >> >> I've been trying to run an umbrella sampling (for the purpose of pmf) >

[gmx-users] umbrella sampling (PMF) position discrepancy

Dear Gromacs users, I've been trying to run an umbrella sampling (for the purpose of pmf) using Gromacs 4.5.5. My system consists of a membrane protein transporter and a Na ion passing through it, from the water bulk on one side of the membrane to the water bulk on the other side. I've used the pr

[gmx-users] g_wham Error bars

Hello everyone, I wanted to ask if anyone knows how to compute standard deviation, for the sake of adding error bars to an energy profile output using g_wham (PMF using umbrella sampling in my case). Just to clarify, I am talking about the deviation of the energy profile on ONE simulation (com