[gmx-users] Re: How long should I run a free energy simulation

[Eudes Fileti]

Hi, I did a little test and I answered myself to the previous question.
I changed the size of the chain for the calculation of the average of dH /
dlambda
(in this case I used a lambda of 0.56). I did time average ranging from 5 to
800ps
and it seems that convergence is achieved in 500ps. I show this link (
http://cromo.ufabc.edu.br/~fileti/web/teste.jpg)
another test, done with a simulation of 60ps and the other with simulations
of 500ps.
The difference is really significant.
Thank you
eef

                                      std. dev.    relative deviation of
                       standard       ---------   cumulants from those of
ps  set      average       deviation      sqrt(n-1)   a Gaussian
distribition
                                                           cum. 3   cum. 4
5   SS1   7.281215e+00   8.698810e+01   1.739762e+00       0.495    0.035
10  SS1  -4.733164e+01   9.785019e+01   1.383949e+00       0.316    0.081
50  SS1  -1.446265e+02   1.259265e+02   7.964448e-01      -0.265    0.137
100 SS1  -1.569191e+02   1.263488e+02   5.650547e-01      -0.283    0.143
150 SS1  -1.705959e+02   1.368184e+02   4.995934e-01      -0.441    0.308
200 SS1  -1.716524e+02   1.394289e+02   4.409153e-01      -0.418    0.206
300 SS1  -1.623856e+02   1.388673e+02   3.585549e-01      -0.411    0.197
400 SS1  -1.566392e+02   1.377266e+02   3.079668e-01      -0.417    0.184
500 SS1  -1.562670e+02   1.365481e+02   2.730968e-01      -0.389    0.133
600 SS1  -1.513204e+02   1.364305e+02   2.490872e-01      -0.373    0.115
700 SS1  -1.500829e+02   1.351678e+02   2.284756e-01      -0.375    0.130
800 SS1  -1.506230e+02   1.350716e+02   2.191153e-01      -0.372    0.121

_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/


On Sat, Nov 22, 2008 at 4:30 PM, Eudes Fileti <fileti at ufabc.edu.br> wrote:

> Hi all,I am performing some free energy test calculations for benzene in
> water. How long should I run a simulation
> so that I get reliable result on my test?
> Thanks
> eef
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC
> Rua Santa Adélia, 166 - Bloco B, Sala 1048
> 09210-170  Santo André - SP Brasil
> +55.11.4437-8408
> skype: eefileti
> http://cromo.ufabc.edu.br/~fileti/
>
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