[gmx-users] Umbrella sampling

Justin Lemkul jalemkul at vt.edu
Fri Nov 24 17:04:45 CET 2017

On 11/24/17 9:14 AM, Rose wrote:
> Hello
> 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?!

Run gmx distance manually. It's probably returning some error, so the 
script fails. I've heard this reported a number of times and no one's 
ever told me what the solution is, so unfortunately there's nothing I 
can do to fix it.

> How did you know for example:
> 50>>>0.6 nm
> 100>>>0.8 nm

This is what gmx distance computes.

> I need deltaz=0.05nm

Then you will need to save frames very frequently. This is a very narrow 
dz, and may be overkill depending on what the system is.

> 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

What force field uses such a cutoff? Don't make ad hoc changes to the 
cutoffs used by any given force field, as you will get unexpected (or 
invalid) results...

> 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?!

You'll have to provide an .mdp file and a complete description of your 
system, how you constructed it, and what your objectives are. Images 
would help.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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