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 Wed Jul 13 2016 - 10:00:03 PDT
