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

Christopher Neale chris.neale at alum.utoronto.ca
Tue May 5 13:13:59 CEST 2015

I see your confusion now.

The PMF is actually defined as dG(x) + C, where C is some unknown constant. Therefore, in the left figure, you have "dG_a(x) + C_a" and on the right you have "dG_b(x) + C_b", so if the profiles have the same shape then the PMFs can be identical if C_a is different from C_b. Subtract 80 from all y-values in the left plot and it will look more like the right plot. For some reason, your WHAM program has placed the minimum at zero in one plot and the maximum at zero in the other plot. I'm guessing the value at minimum x gets set to zero.


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: 04 May 2015 21:50
To: gromacs user_list
Subject: Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Thanks for the advice

I will do this exercise with other molecule and will let you know the results.
but, why i was confused is because in one PMF curve all the free energy values are on the positive side where as the other has all free energy values on the negative side. do these signs are not important or there is something else. As What I understand is that if the free energy of the drug increases when going to the center of the bilayer, this drug cannot passively diffuse across the membrane (thermodynamically unfavored ).
I will try to go through more literature on this topic to understand this concept in more detail.

thanks you

with regards
Mahender Singh

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