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 <[email protected]
<mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>>
*To:* [email protected] <mailto:[email protected]>
*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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