Thank you Amy and Christina.
I had already read the manual but my doubt is more about what there will be
in x and in y.
For example, having a look at the two output files that I attached before I
think (correct me if I am wrong) that I had in the second column the
reaction coordinate and in the third one the potential energy. So how can I
combine the first reaction coordinate with the second?
On Wed, Jul 13, 2016 at 10:55 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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Received on Thu Jul 14 2016 - 03:00:02 PDT
