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

[Christopher Neale]

Take a look at profiles in the literature for arginine across a bilayer. It has a maximum at the center. Probably true for any molecule with a large charge/molecular weight ratio. For more help you'd likely have to reveal your system and provide an image of the PMF. However, there is no reason to think that you've got a problem unless you're working with a small hydrophobic molecule (in which case the dG should almost certainly be the inverse of what you see). One test you can do is to compare the free energy of solvation of your molecule in water and octane using the double-decoupling method.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of mahender singh <pharmbiochem at live.com>
Sent: 03 May 2015 01:07
To: gromacs user_list
Subject: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

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

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