[gmx-users] mdp-settings for charmm36 and lipid apl values

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

Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

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 jalem...@vt.edu On 5/8/13 11:09 AM, Gmx QA wrote: Hi gmx-users, I've

[gmx-users] Re: Force vs distance plot in pulling simulation?

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

Re: [gmx-users] Re: Umbrella sampling question

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 in the profile.xvg-file should correspond to something I could measure with g_dist. Turns out it does

Re: [gmx-users] Re: Umbrella sampling question

) 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 er...@xray.bmc.uu.se Hi, See below. 14 nov 2012 kl. 15.06 skrev Gmx QA: Hi Chris, and thank you for your reply

[gmx-users] Re: Umbrella sampling question

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

[gmx-users] Re: Umbrella sampling question

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