[gmx-users] Umbrella sampling

Rose rose.rhmn93 at gmail.com
Fri Nov 24 15:15:12 CET 2017


I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as I'm not good in programming I couldn't understand what happened there?!
How did you know for example:
50>>>0.6 nm
100>>>0.8 nm

I need deltaz=0.05nm 

Please help me, i don't know where should i find these informations and modify them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab.
What is my mistake?!

I really need your help.

Best Regards


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