[gmx-users] Umbrella sampling

[Justin Lemkul]

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

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

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