[gmx-users] Zero Potential of Mean Force with g_wham
susietomasio at gmail.com
Wed Mar 9 15:43:15 CET 2011
Thank you Jianguo.
So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1?
On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:
> I met the same problem when using 4.5.1 for some systems, the PMF shows
> zero curve, while the hist file looks fine. The problem disappears when
> using 4.5.2.
> *From:* Susana Tomasio <susietomasio at gmail.com>
> *To:* gmx-users at gromacs.org
> *Sent:* Wednesday, 9 March 2011 20:07:25
> *Subject:* [gmx-users] Zero Potential of Mean Force with g_wham
> Dear all,
> I am running umbrella sampling of a molecule through a lipid bilayer with
> gromacs 4.5.1.
> When I extracted the potential of mean force with g_wham I got zero for all
> the windows.
> Any ideas of why this is happening?
> This is the command I used:
> g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist
> And this is the pull code of my .mdp file:
> ; Pull code
> pull = umbrella
> pull_geometry = position
> pull_dim = N N Y
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = Bilayer
> pull_group1 = Protein
> pull_vec1 = 0 0 0
> pull_init1 = 0 0 0
> pull_rate1 = 0
> pull_pbcatom0 = 1453
> pull_pbcatom1 = 13187
> pull_k1 = 3000 ; kJ mol^-1 nm^-2
> pull_nstxout = 1000 ; every 2 ps
> pull_nstfout = 1000 ; every 2 ps
> Thank you.
> Best regards,
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