[gmx-users] pmf

[Alex]

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

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).

Thanks very much in advance.

Regards,
Alex