[gmx-users] PMF - Protein-Me​brane

2012-08-15 Thread Christopher Neale
The large magnitudes of orthogonal barriers in such systems will lead to both systematic and statistical sampling errors that motivate the application of both approaches, preferably repeated a few times each. So I think that Justin is right, in an idealized situation. I might modify his

[gmx-users] PMF - Protein-Me​brane

2012-08-10 Thread dariush
Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane complex and pull out protein to separate

Re: [gmx-users] PMF - Protein-Me​brane

2012-08-10 Thread Justin Lemkul
On 8/10/12 11:18 AM, dariush wrote: Hi All, I have a question regards to PMF: Consider we are sure one protein will bind to membrane after 100ns in MD run and make a complex. Instead of pulling protein to membrane to calculate PMF, can we start from last configuration of protein-membrane