[gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF

Justin Lemkul jalemkul at vt.edu
Tue Nov 13 00:54:17 CET 2018

On 11/8/18 12:12 PM, CROUZY Serge 119222 wrote:
> Hello Justin
> I still don't understand where Gromacs takes the x coordinates in the output pmf with g_wham
> If I run g_wham with tpr-files and pullf-files without the pullx-files
> -it tpr-files.dat -if pullf-files.dat
> I get a profile which means that g_wham does not take the X-coordinates in the pullx (I don't give them), but in the tpr files ...
> So what X-coordinates are stored in the tpr-files ?

The only coordinates in a .tpr file are those from the coordinate file 
used to build that .tpr file.

This is why I really don't understand what's going on, and it's largely 
impossible for me to provide any additional, useful advice without being 
provided input files (at least .mdp snippets) and the actual output 
you're getting. The absolute positions should be meaningless. The only 
values that matter are displacements along the reaction coordinate 
(pullx) or forces on the biasing potential (pullf), either of which are 
used to equivalently construct a PMF profile.

> Then if I use
> -it tpr-files.dat -ix pullx-files.dat
> Where does g_wham take the forces and which x coordinates does it take : those from the tpr or those from the pullx ?

See above.

> Moreover when I restart my simulations, I regenerate new tpr files
> For instance to add 10 more ns
> gmx convert-tpr -s umbrella10ns.tpr -extend 10000 -o umbrella20ns.tpr
> gmx mdrun -s umbrella20ns.tpr -cpi xxx.cpt ....
> If I run g_wham after this simulation, which tpr should I use ?

The difference is irrelevant, and the .tpr files differ only in the 
number of steps specified, which is information that is not used by gmx 
wham. The only information that gmx wham should be reading is the 
information related to the pull code (geometry, number of coordinates, 
force constant(s), etc.)


> Can you please explain the role of these tpr in g_wham calculations?
> Thanks a lot
> On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote:
>> Hello Justin-
>> In MY pullx first column is Time and second column is absolute
>> coordinate of the COM of the pulled group Maybe we are missing an option which would print X and dX in the pullx files - one of the pull-print stuffs ???!!.. In that case too bad we would have tons of "bad" pull files Printing the reaction coordinate (dX) should be the default .. Don't you think so ?
>> Hence my problem with wham using absolute coordinate instead of actual
>> distance between the two centers of mass What do you suggest to retrieve the actual values of my reaction coordinate without rerrunning everything ?
> It should be straightforward to apply a systematic shift to the values in the output PMF curve. But I don't know how you've set up your pull code to get such output in the first place. The absolute position of
> group0 should be totally irrelevant.
> -Justin
>> Serge
> *************************


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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