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

[Susana Tomasio]

Hi,

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.

Susana

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
> issues.
>
> Mark
>
>
>
> 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
>>
>>
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>
>
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