Re: umbrella sampling

From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jul 12 2012 - 07:46:50 CDT

you could still do COM with fewer atoms, just pick the C-aplha atoms in
that segment. You probably picked a lot of hydrogens, which are nearly
meaningless anyway.

I'm not sure if there is a script for umbrella sampling, maybe, but
umbrella sampling is quite simple, you give a fixed center for the harmonic
restraint, and run the simulation for some time, then you give a different
center and repeat. I think what you have setup will move the center over
time, which you won't be able to analyze with WHAM.

~Aron

On Thu, Jul 12, 2012 at 2:17 AM, ipsita basu <ibasu788_at_gmail.com> wrote:

> Thank you very much sir for your reply.
> I actually want to select the COM of a segment of protein that's why I
> choose all the atoms in that segment.
> By 400 MD steps I wanted to mean the timestep during which the
> z-distance will reduce by the width value. And I will correct it
> according to your suggestion.
>
> And I didn't want an isotropic distance, I just want to set the
> variable as z distance between the selected group 1 and group2.
>
> And sir you said that this is an input of steered MD, I didn't find a
> seperate script for umbrella sampling in the NAMD tutorial. Is there
> anything else?
>
> Thank you again.
>
> On 7/11/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> > Ipsita,
> >
> > First, your variable involves several thousand atoms. Do you really
> > need so many? This could slow down the calculation dramatically. Try
> > to express the same quantity using a smaller number of atoms (e.g.
> > picking just one atom per molecule or per residue).
> >
> > Your input describes a form of steered MD calculation, and an
> > extremely fast one: the restraint will move all the way in only 400 MD
> > timesteps. Maybe you intended to do slower steering, or maybe you
> > wanted to split the transition into 400 stages? See targetNumStages in
> > the documentation for details.
> >
> > Your variable describes an isotropic distance. Did you want to look at
> > a z projection instead? If yes, see the distanceZ component in the
> > doc.
> >
> > Finally, unlike in "traditional SMD", you don't need position
> > restraints because the variable is an internal coordinate of the
> > system. It is independent of global translations.
> >
> > Best,
> > Jerome
> >
> >
> > On 11 July 2012 13:48, ipsita basu <ibasu788_at_gmail.com> wrote:
> >> Sir,
> >> I want to umbrella sampling in my membrane protein simulation to
> >> calculate potential mean force. My colvar configuration file is:
> >> colvarsTrajFrequency 200
> >> colvar {
> >> name length
> >> distance {
> >> group1 {
> >> atomNumbersRange 94313-98031
> >> }
> >> group2 {
> >> atomNumbers 1503 2307 2709
> >> }
> >> }
> >> }
> >> harmonic {
> >> name lenpot
> >> colvars length
> >> centers 17.0
> >> forceConstant 1.0
> >> targetCenters 80.0
> >> targetNumSteps 400
> >> }
> >>
> >> I want to vary the z-distance between group 1 and group 2.
> >> I put the initial zav value of group 1 in centers (centers 17.0)
> >> and the zav value of group in targetCenters.
> >> Now I am just a beginner in umbrella sampling and I've some queries
> >> about this. My questions are:
> >> 1. Is that right what I'm doing or I misunderstood?
> >> 2. What should be the value of targetNumsteps? Is it should be the
> >> value during which the distance will reduce by the given width?
> >> 3. should the rest system will be position restrained?
> >>
> >> Any type of help will be really appreciated.
> >> If the questions are bizarre then I'm sorry.
> >>
> >> Thanking you,
> >> Yours faithfully
> >> Ipsita
> >> --
> >> Ipsita Basu
> >> Research Fellow
> >> c/o : Dr. Chaitali Mukhopadhyay
> >> Rajabazar Science College
> >> 92 APC Road
> >> Kolkata - 700009
> >>
> >
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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