[gmx-users] pmf

[Justin Lemkul]

On 10/28/16 4:04 PM, Alex wrote:
> Dear Gromacs user,
>
> Below are the result of PMF simulation of a peptide adsorbed into a solid
> surface.
> Would you please comment on them in order to improve the result.
>
> The force constant in the umberela sampling is 1100.
> For each windows:  1.2 ns NVT equilibration followed by 2 ns of NPT and 15
> ns of NVT produciton run.
> Should I change the force constant or increase the simulation time for each
> windows or just increasing the sampling in some region?
>
>
> https://drive.google.com/open?id=0B_CbyhnbKqQDMkpLc0didlMxTWs
>
> https://drive.google.com/open?id=0B_CbyhnbKqQDZ1RpT3JxMjdyazA
>

You need more windows.  You have obvious gaps in several parts of the reaction 
coordinate.

> https://drive.google.com/open?id=0B_CbyhnbKqQDZlR4RGVIWk5KbVU
>
> It is just one dimension pulling by "N N Y" by pull-coord1-geometry =
> distance, then I was also wondeing why my pullx.xvg files has more than
> normal column so that gmx wham complain with error about it:
> Fatal error:
> Using 1 pull coodinates from prdd.0.tpr,
>  but found 4 data columns in pullx-prd.0.xvg (expected 3).
>

What version of GROMACS is this?  Is the version of gmx wham the same as the 
version of grompp/mdrun used to create/run the simulations?  I would expect 4 as 
well (COM x,y,z of reference and z-coordinate of pulled group), but there have 
been a lot of changes to the pull code in recent versions.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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