[gmx-users] Pull Simulation: Force spike on F vs X output and extension stall

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Tue Aug 16 13:22:30 CEST 2011


I was wondering if you would be able to clear up a slightly confusing aspect of the simulations I've been running.

I am currently performing a pull simulation and when viewing the outputs of all the simulations I have run I see the extension of the protein stop when it reaches the same sub-domain each time (at around a 10 nm extension).  The mdp file I use as the input file states that the pull distance should be much larger than this.

Also when viewing the -px -pf outputs this agrees.  When the simulation reaches a 10 nm extension it stops and only increases around 0.2 nm over the remaining simulation time (~3000 ps). When force extension is plotted there is still an increase in force which results in a spike at the 10 nm extension point, increasing the force from around 0.7 nN to around 30 nN.

Is there any reason this could be an artefact or is it just the fact that this domain is very firmly in contact with it's adjacent domain?

Thank you for your help with this matter.

Kind regards,


Natalie Stephenson, B.Sc
PhD Research Associate

Manchester Interdisciplinary Biocentre
131 Princess Street
M1 7DN
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