Membrane=nan±nannm^2 results....?

[sergio-garay]

Hi all

I have a gromacs membrane simulation composed by DPPC and chol, when I run fatslim it does not give any error but:

[sgaray@localhost Adrian]$ fatslim apl -c 250_300ns_dt100_16dyn.gro -n index.ndx -t trj_250_300ns_dt100_16dyn.xtc --plot-apl dppc_chol_area FATSLiM - Fast Analysis Toolbox for Simulations of Lipid Membranes version 0.2.1 Copyright (c) 2013-2016 Sébastien Buchoux

Running command: 'apl'... This may take some time, be patient! Analysis will be performed using 8 threads. Analysing frame 501/ 501 (time: 300000 ps)... done in 9 ms (Remaining: 0 s) Results: Average values over 501 processed frames: Area per lipid: Membrane=nan±nannm^2 - Outer leaflet=nan±nannm^2 - Inner leaflet=nan±nannm^2 Area per lipid values saved to 'dppc_chol_area.xvg'

Area: Membrane=nan±nannm^2 - Outer leaflet=nan±nannm^2 - Inner leaflet=nan±nannm^2

DEBUG! 'apl' command executed in 4.480 s (CPU) Goodbye!

Could you give any clue of what is happening? Am I doing something wrong? Thank you in advance

[seb-buch]

Hi,

This bad behaviour could be either be due to a bug or a badly defined headgroup index. It is hard to tell without seeing the input files. Is it possible for you to send me (via email) your .gro and .ndx files?

[sergio-garay]

No problem, here they go.

Thank you for your help.

Sergio

On Thu, Apr 26, 2018 at 6:26 AM, Sébastien Buchoux <notifications@github.com

wrote:

Hi,

This bad behaviour could be either be due to a bug or a badly defined headgroup index. It is hard to tell without seeing the input files. Is it possible for you to send me (via email) your .gro and .ndx files?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/FATSLiM/fatslim/issues/4#issuecomment-384574496, or mute the thread https://github.com/notifications/unsubscribe-auth/AjdUlmWpFqcGIhgXL7PjeKmJyGQ5AXNIks5tsZLAgaJpZM4TgeHx .

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Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221

[seb-buch]

Github apparently stripped your message down as there is no attachments... Could you send them directly using my email (see my github profile page) rather than replying to github email notification?

thanks