Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-12 Thread Justin A. Lemkul
Steven Neumann wrote: On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrot

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-12 Thread Steven Neumann
On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Hi Justin, >> As you advised I reduced number of my windows and

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-12 Thread Steven Neumann
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Justin, >> As you advised I reduced number of my windows and I obtined histogram: >> http://speedy.sh/2b9dT/histo.**JPG >> Which looks really good. >> The correspond

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-12 Thread Justin A. Lemkul
Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.__JPG

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-11 Thread Justin A. Lemkul
Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-11 Thread Steven Neumann
Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond to everything above 0 kcal/mol

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-08 Thread Steven Neumann
On Thu, Mar 8, 2012 at 2:18 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Gmx Users, Dear Justin, >> I pulled my ligand away from my protein. Ligand was attached to lower >> part of my protein, I pulled in Z coordinate it using: >> >> ; Run parameters >> >> integrator = md ;

Re: [gmx-users] Umbrella Sampling - Ligand Protein

2012-03-08 Thread Justin A. Lemkul
Steven Neumann wrote: Dear Gmx Users, Dear Justin, I pulled my ligand away from my protein. Ligand was attached to lower part of my protein, I pulled in Z coordinate it using: ; Run parameters integrator = md ; leap-frog integrator nsteps = 500 ; 2 * 500 = 10 ns dt = 0.002 ; 2 f