[gmx-users] Zero Potential of Mean Force with g_wham

[Mark Abraham]

On 10/03/2011 1:43 AM, Susana Tomasio wrote:
> Thank you Jianguo.
>
> So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1?

Quite likely. Check the change logs on the GROMCACS website for relevant 
issues.

Mark

>
> Best regards,
>
> Susana
>
>
>
> On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li <ljggmx at yahoo.com.sg 
> <mailto: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.
>     Jianguo
>
>     ------------------------------------------------------------------------
>     *From:* Susana Tomasio <susietomasio at gmail.com
>     <mailto:susietomasio at gmail.com>>
>     *To:* gmx-users at gromacs.org <mailto: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,
>
>     Susana
>
>
>     --
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