Re: [gmx-users] Pulling ion - US

2012-12-10 Thread Justin Lemkul
On 12/10/12 10:50 AM, Steven Neumann wrote: Would you also specify in each US window specific residue instead of the whole protein? That really depends on whether the residue-ion distance reflects the desired reaction coordinate and if doing so is superior to using the protein-ion distance

Re: [gmx-users] Pulling ion - US

2012-12-10 Thread Steven Neumann
Would you also specify in each US window specific residue instead of the whole protein? Sreven On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann wrote: > On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul wrote: >> >> >> On 12/10/12 9:01 AM, Steven Neumann wrote: >>> >>> Dear Gmx Users, >>> >>> I am

Re: [gmx-users] Pulling ion - US

2012-12-10 Thread Steven Neumann
On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul wrote: > > > On 12/10/12 9:01 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am pulling away cation from the protein glutamic acid residue with: >> >> pull= umbrella >> pull_geometry = distance ; simple distance increase >> pul

Re: [gmx-users] Pulling ion - US

2012-12-10 Thread Justin Lemkul
On 12/10/12 9:01 AM, Steven Neumann wrote: Dear Gmx Users, I am pulling away cation from the protein glutamic acid residue with: pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance