[gmx-users] Umbrella sampling and WHAM along a curved pathway?

[HAO JIANG]

Hi, Jochen,

Thanks a lot for your reply. I looked at the example header provided
by g_wham -h. I just wonder if you can answer some more questions for
me.

The example header is

# UMBRELLA      3.0
# Component selection: 0 0 1
# nSkip 1
# Ref. Group 'TestAtom'
# Nr. of pull groups 2
# Group 1 'GR1'  Umb. Pos. 5.0 Umb. Cons. 1000.0
# Group 2 'GR2'  Umb. Pos. 2.0 Umb. Cons. 500.0
#####

I guess following "# Component selection" one need to specify the
Cartesian coordinate components in which the distance restraints are
applied. In this example, I guess the restraint is applied in the Z
coordinate, right? If, say, I want to put restraints in all three
coordinates, X,Y, and Z, I need to put "1 1 1" here, right? In this
case, there shall be 3 coordinates to specify the Umb.  Pos., so I
would put something like  "# Group 1 'GR1'  Umb. Pos. 5.0 5.0 5.0 Umb.
Cons. 1000.0", assuming the force constant is same for X, Y, and Z. Am
I right, or is there some other way to specify the position of the
umbrella?  And I should have 1 time column and 3 data
columns/per-group following the headers, right?

If, instead of using the pull code, I create by hands a set of initial
configurations where the pull-groups are placed along a curved
pathway,   and use "pull_start      = yes" with "pull_rate1      = 0",
will GROMACS and g_wham automatically recognize the positions of the
umbrellas from the initial configurations?

Thank you very much!

Hao


On Thu, Feb 16, 2012 at 10:42 AM, Jochen Hub <jhub at gwdg.de> wrote:
> Hi,
>
> since there is no pull type for curved pathways, you have to generate the
> gmx3-type pdo files from your simlation output and use these in g_wham
> (g_wham -ip). See g_wham -h for a example header of a pdo file.
>
> Cheers,
> Jochen
>
>
>
> Am 2/14/12 5:53 PM, schrieb HAO JIANG:
>
>> Dear all,
>>
>> I would like to calculate the PMF along a curved reaction pathway
>> using umbrella sampling. I just wonder if it is appropriate to use
>> g_wham to extract the PMF along the curved pathway? Any help would be
>> appreciated.
>>
>> Hao Jiang
>
>
> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.de/
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