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

[Susana Tomasio]

Thank you Jianguo.

So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1?

Best regards,

Susana



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.
> Jianguo
>
>  ------------------------------
> *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,
>
> Susana
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110309/f80215ed/attachment.html>