Re: [gmx-users] fail to pull

2013-04-07 Thread Jianguo Li
You switched on the position restraint in your mdp file, is that the reason? From: Albert To: gromacs maillist Sent: Sunday, 7 April 2013, 2:47 Subject: [gmx-users] fail to pull Dear: I am trying to pull my ligand outside of the binding pocket with

Re: [gmx-users] fail to pull

2013-04-07 Thread Albert
IC. thanks a lot for explanations. Albert On 04/07/2013 06:08 PM, Justin Lemkul wrote: I'm assuming you're getting that line from my tutorial. You pass the .cpt file to grompp to preserve velocities from the previous equilibration phase. If you don't, what was the point of equilibrating? Coor

Re: [gmx-users] fail to pull

2013-04-07 Thread Justin Lemkul
On Sun, Apr 7, 2013 at 12:05 PM, Albert wrote: > hello Justine: > > thanks a lot for such kind comments. > > I may find the problem, the COM probably is not suitable to use whole > protein since I found by g_dist that all the distance are between 0.9-1.0 > nm throughout the whole pulling proces

Re: [gmx-users] fail to pull

2013-04-07 Thread Albert
hello Justine: thanks a lot for such kind comments. I may find the problem, the COM probably is not suitable to use whole protein since I found by g_dist that all the distance are between 0.9-1.0 nm throughout the whole pulling process. BTW, I notice that we are using command: grompp -f

Re: [gmx-users] fail to pull

2013-04-07 Thread Justin Lemkul
On Sun, Apr 7, 2013 at 11:17 AM, Albert wrote: > On 04/06/2013 08:52 PM, Justin Lemkul wrote: > >> Hard to tell. Does your ligand have a suitable exit pathway exactly >> aligned >> along the x-axis? Have you tried increasing the pull rate? How long is the >> simulation? I don't even see nsteps in

Re: [gmx-users] fail to pull

2013-04-07 Thread Albert
On 04/06/2013 08:52 PM, Justin Lemkul wrote: Hard to tell. Does your ligand have a suitable exit pathway exactly aligned along the x-axis? Have you tried increasing the pull rate? How long is the simulation? I don't even see nsteps in the above .mdp file. How about increasing the force constant?

Re: [gmx-users] fail to pull

2013-04-06 Thread Justin Lemkul
On Sat, Apr 6, 2013 at 2:47 PM, Albert wrote: > Dear: > > I am trying to pull my ligand outside of the binding pocket with > following configurations: > > title = Umbrella pulling simulation > define = -DPOSRES > ; Pull code > pull= umbrella > pull_geometry = distance ;

[gmx-users] fail to pull

2013-04-06 Thread Albert
Dear: I am trying to pull my ligand outside of the binding pocket with following configurations: title = Umbrella pulling simulation define = -DPOSRES ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start