[gmx-users] Umbrella Pulling
s.neumann08 at gmail.com
Mon Feb 20 21:01:51 CET 2012
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Steven Neumann wrote:
>> On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>> Steven Neumann wrote:
>> Dear Justin and Gmx Users,
>> I run a pulling of my ligand away from my protein with the same
>> mdp file and I obtained two different plots - Force vs time (The
>> breaking point occured at different times with different force).
>> Can you please explain?
>> If you change the stiffness of the spring, you change the magnitude
>> of the applied force. Thus, the behavior you see will occur either
>> faster or slower, depending on the strength of the spring.
>> So how can I change the stiffness of my spring?
> By changing pull_k1. I thought that's what you meant you had already
> done, but I can see now that my interpretation wasn't correct. Understand
> the SMD is a non-equilibrium, path-dependent process. I don't know what
> you're pulling from what, but if the interactions are slightly different
> along the dissociation pathway, the forces are different because the path
> is different.
> I used exactly the same mdp file with the same parameters - the same same
pull_k1 as well and I obtained different plots. The starting configuration
is also the same. I pull a ligand away from the protein.
Would you obtain from two normal MD or SMD simulations with the same
starting configuration different results?
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users