Thanks Justin, those are good points.
A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?
THANKS
2013/5/8 Justin Lemkul
>
>
> On 5/8/13 11:09 AM, Gmx QA wrote:
>
>> Hi gmx-user
Hi gmx-users,
I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input nonetheless :-)
The relevant section
Hi Erik and Justin
Thanks, writing such a script is easy.
The point of it all would be to be able to map the magnitude of the pulling
force to what I see happen in the pulling simulation. How else would you
get an understanding of what the pulling force means?
Thanks
/PK
>
> > The only solution
oice of pull_pbcatom0 should not
> matter as long as the choice allows to figure out how to handle the
> periodicity.
>
> Best,
>
> Erik
>
> 15 nov 2012 kl. 19.56 skrev Gmx QA:
>
> > Hi Chris
> >
> > Seems my confusion was that I assumed that the distances
Hi Chris
Seems my confusion was that I assumed that the distances in the
profile.xvg-file should correspond to something I could measure with
g_dist. Turns out it does not.
Thank you for helping me sorting out this, I got it now :-)
About pull_pbcatom0 though. My box is >> 2*1.08 nm in all direct
t) to relate (a) events and
structures in individual frames (or in the pulling simulation) to (b) the
pull force vs time plot and (c) the PMF-plot.
Thanks
/PK
2012/11/14 Erik Marklund
> Hi,
>
> See below.
>
> 14 nov 2012 kl. 15.06 skrev Gmx QA:
>
> > Hi Chris,
> >
> &g
Hi Chris,
and thank you for your reply. I should have included my g_dist command in
my first mail. Here goes:
I first run trjconv to extract the individual frames from my pulling
trajectory
$ trjconv -f pull.xtc -s pull.tpr -o conf.gro -sep -pbc mol -ur compact
Then, g_dist like so:
$ g_dist -s
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