Re: [gmx-users] toluene tutorial sc-power value

Fine :) So forget what I wrote before...I mentioned exactly that :) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette

Re: [gmx-users] toluene tutorial sc-power value

hi 10 points is strange ;) 11 is the number with equally spaced points. ANyway, it should suffice to get a more or less proper number. I guess, they use simpsons integration, what should be ok. I compared my scripts results, which uses simpson, with those of xmgrace and they fit. The longer you

Re: [gmx-users] toluene tutorial sc-power value

Hi maik I made the calculation with sc-power=2 adding 3 lambda values. Now i get integrating the plot of average free energy for the mutation of toluene in water 0.559 instead of 15,8 in previous calculation. if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1 KJ/mol exp.). This

Re: [gmx-users] toluene tutorial sc-power value

hi concerning the cycle i saw this error since i started the tutorial, i paid attention to that but as you said it's not that important since my energy value is too high. i'm right now doing the problem again with sc-power=2 and also 10 points is it enough to have an approximate correct value sinc

Re: [gmx-users] toluene tutorial sc-power value

I had a veeery short look into the tutorial and found an error. DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong. The correct cycle would be: DG_1+DG_3=DG_hyd+DG_2 =>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0 So its: DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3 Anyway, this won't help you, cause the onl

Re: [gmx-users] toluene tutorial sc-power value

Hi maik the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water) for fisrt one deltaG_mutation(vacuo) =-2,85 for second deltaGmutation(water) =15,87 so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol i'll do a series of calculation with sc-power=2 and see the difference see if

Re: [gmx-users] toluene tutorial sc-power value

Hi Now, make sure, that you apply the thermodynamic cycle correctly. I wouldn't wonder about large errors. Depending on the definition of large. Error estimation from free energy calculations can be very tricky. Using mpi shouldn't influence your calculations outcome. Still I don't know the er

Re: [gmx-users] toluene tutorial sc-power value

Hi MaiK, Sorry i forgot the subject. Thank you to have answered this email. This tutorial is about solvation free energy of toluene using thermodynamical cycles. two energies have to be calculated according to this cycle, the hydration energy of toluene and the mutation energy from dummy to toluene