[gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

[mahender singh]

Hello
good morning to all

I did steered md simulation by using following code
;pull code
 pull        = umbrella
 pull_geometry    = direction
 pull_dim    = N N Y
 pull_coord1_vec    =0 0 1
 pull_start    = yes 
 pull_ngroups    =2
 pull-ncoords    =1
 pull_coord1_groups    = 1 2
 pull_group1_name    = NPROT_ref
 pull_group2_name    = LIG 
 pull_coord1_rate    = 0.004        ; 0.004 nm per ps = 4 nm per ns
 pull_coord1_k        = 1000        ; kJ mol^-1 nm^-2
 pull_nstxout    = 500        ; every 1 ps
 pull_nstfout    = 500        ; every 1 ps

And then used these results of SMD for umbrella sampling (total umbrella window =30 across the membrane) by using following code

 pull        = umbrella
 pull_geometry    = direction
 pull_dim    = N N Y
 pull_coord1_vec    =0 0 1
 pull_start    = yes 
 pull_ngroups    =2
 pull-ncoords    =1
 pull_coord1_groups    = 1 2
 pull_group1_name    = NPROT_ref
 pull_group2_name    = LIG 
 pull_coord1_rate    = 0.0
 pull_coord1_k        = 1000        ; kJ mol^-1 nm^-2
 pull_nstxout    = 500        ; every 1 ps
 pull_nstfout    = 500        ; every 1 ps

In my case, I am moving a molecule from -z to +z across the membrane. So I used pull-geometry=direction in gromacs 5.0.4 (as per gromacs site= http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force), as I cannot use pull-geimetry=distance. Every thing completed correctly (seems to me), but when I used gmx wham on the pullf.xvg files, PMF profile was on the positive side. PMF increased from 0 (bulk water) to 60 at the center of the membrane and than again decreased to the 0 (bulk water on the other side).
I all the literature, PMF values for the molecule crossing a membrane is on the negative side and minimum at the center.
I am confused about the result. Did I do something wrong with the parameters or understanding the PMF curve wrongly.

can any one give their suggestion on this.

thanks in advance of user time and help.

with regards
Mahender Singh