Hi Alessandra,
Have you taken a look at the WHAM manual? It can be found on the Grossfield
Lab website (
http://membrane.urmc.rochester.edu/content/wham). The manual
does an excellent job of explaining the various command line options needed
to run 2d WHAM and the correct format for the input file.
On Wed, Jul 13, 2016 at 11:55 AM, Alessandra Lacetera <
alessandra.lacetera.gmail.com> wrote:
> Hello,
> I have performed an umbrella sampling to study a reaction in which there is
> a formation of an OH (O from a glutamate and the H from a water molecule,
> reaction 1) and then the nucleophilic attack of the hydroxide to a
> phosphate group (reaction 2). So first I run a script for the first
> reaction coordinate scan, using a step of 0.2 A and a force constant of 100
> kcal/mol defining in this way the reaction coordinate:
>
> rc_iat="iat=44916, 44918, 44918, 1527, rstwt=1,-1"
>
> And with these keywords
>
> &wt type='DUMPFREQ', istep1=1 /
> &wt type='END' /
> DISANG=rc0.0.RST
> DUMPAVE=rc0.0_1.tra
>
> I had this output file (for e.g. rc0.0_1.tra)
>
> 0 -0.355 3.617
> 1 -0.255 3.620
> 2 -0.119 3.623
> 3 -0.003 3.628
>
> The second reaction coordinate scan was performed fixing the first reaction
> coordinate, using a step of 0.2 A and a force constant of 100 kcal/mol
>
> &rst
> iat=44916,44918, 44918, 1527, rstwt=1,-1
> r1=0.0,r2=0.0,r3=0.0,r4=500,
> rk2=50,rk3=50,
>
> The output file was like:
>
> 0 1.719 -2.359
> 1 1.723 -2.362
> 2 1.726 -2.369
> 3 1.728 -2.381
>
> It is not clear to me how to use wham-2D for crossing all the results for
> generating the PMF and how to write a proper metadata file. In the tutorial
> http://ambermd.org/tutorials/advanced/tutorial17/section3.htm, wham is
> used, but not wham-2d and I was wondering if the metadata should be
> different. Could you help me or point me to any tutorial about how to
> generate the PMF?
>
> Thank you in advance
>
> --
> Alessandra Lacetera
> PhD Student CIB (CSIC)
> Calle Ramiro de Maetzu, 9
> 28040, Madrid - Spain
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Wed Jul 13 2016 - 10:30:02 PDT
