[gmx-users] umbrella Sampling and PMF- Error estimation

2013-07-31 Thread Mohsen Ramezanpour
Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Thanks in advance for any

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

2013-07-31 Thread Justin Lemkul
On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

2013-07-31 Thread Mohsen Ramezanpour
Thank you for your reply Dr. Justin On 7/31/13, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella

Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

2013-07-31 Thread Mohsen Ramezanpour
Dear Dr.Justin I read that article, It was very helpful. Thanks a lot. After using g_wham with bootstrapping options. I have got an averaged PMF profile (like Fig.2C in that article) and an standard deviation (like Fig.2D In that article) which obtained in this way. As you see, the standard

Re: Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

2013-07-31 Thread Justin Lemkul
On 7/31/13 10:19 AM, Mohsen Ramezanpour wrote: Dear Dr.Justin I read that article, It was very helpful. Thanks a lot. After using g_wham with bootstrapping options. I have got an averaged PMF profile (like Fig.2C in that article) and an standard deviation (like Fig.2D In that article) which