From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a large pull force (say 2500) and then looking at the pullf.xvg gives you the max peak, which you just set it slightly over this, mine was higher than published as the protein had more affinity, if you set it too low it just acts like a horminic oscillator...with the rate, I found if there is no force, only rate, it doesn't do anything pulling apart something with a high affinity, with a small molecule the pull rate worked (I only tried this a couple times)...somone may have better suggestions,
Stephan Watkins
Gesendet: Dienstag, 09. Juli 2013 um 18:56 Uhr
Von: rookie417 <lsura...@tulane.edu>
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling- force vs time plots
Von: rookie417 <lsura...@tulane.edu>
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling- force vs time plots
Hello all,
I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:
pull=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000
After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an
ideal force-time plot look like and does the choice of pull_k1 affect the
histogram? It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.
Thanks a lot.
Andy
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I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer over a distance
of 5nm:
pull=umbrella
pull_geometry=direction
pull_vec1=1 0 0
pull_start=yes
pull_ngroups=1
pull_group0=surf
pull_group1=poly
pull_rate1=0.01
pull_k1=1000
After the simulation, pullf.xvg plot I obtained is a linearly increasing
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not
sure if this is right. My question is, on what basis do we select the
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a
choice of parameters as long as the system does not deform? How does an
ideal force-time plot look like and does the choice of pull_k1 affect the
histogram? It appears, the entire procedure depends on the choice of input
of these two variables. I would greatly appreciate if someone can explain
this concept.
Thanks a lot.
Andy
--
View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-force-vs-time-plots-tp5009709.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list gmx-users@gromacs.org
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* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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