Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Laura Kingsley
There is a way to extract the PMF from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html - Laura On 10/31/2011

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Sanku M
WHAM based on the data set on umbrella sampling. Sanku From: Laura Kingsley lking...@purdue.edu To: gmx-users@gromacs.org Sent: Monday, October 31, 2011 11:09 AM Subject: Re: [gmx-users] Jarzinsky's inequality from SMD simulation There is a way to extract

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Laura Kingsley
Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. On 10/31/2011 01:29 PM, Sanku M wrote: using SMD simulation. What is does that

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Justin A. Lemkul
Laura Kingsley wrote: Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. One approach: