[gmx-users] Zero Potential of Mean Force with g_wham
susietomasio at gmail.com
Wed Mar 9 17:53:50 CET 2011
I ran g_wham 4.5.2 and did get a non-zero PMF curve.
I assume that there is something going on with g_wham on version 4.5.1.
Thank you for your help.
On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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
> Best regards,
> 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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