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

CROUZY Serge 119222 serge.crouzy at cea.fr
Thu Nov 8 18:12:17 CET 2018

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 ?

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 ?

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 ?

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.


> Serge

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