You may also want to look at www.alchemistry.org, as it has some general information about how these should be set up.
On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > Again, *please keep all Gromacs-related correspondence on the mailing list* > The type of information that you have posted is important to share with > others who may know how to help. I do not know the answer to your problem. > I would suggest contacting the list again with the following information: > > 1. The relevant contents of your .mdp file(s) > 2. What each figure in your image represents (main image vs. inset) > > -Justin > > Eudes Fileti wrote: >> >> Justin thanks for the reply. Sorry, 160000 refers to the value of dg / dl >> for lambda = 0. I am sending you a link for you see the profile of the >> curve. >> http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg >> This case is for solute in benzene. The peak in lambda=0 is around 30000. >> For sc-power=1 I got a peak much higher than for sc-power=2, and therefore >> the integration in this case (sc-power=1) could lead me to a much greater >> error. In both cases (ethanol and benzene) the curves coincide for values of >> lambda beyond 0.4. >> bests >> eef >> >> P.S.: I am using the 3.3.3 version. >> >> _______________________________________ >> 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 Wed, Mar 18, 2009 at 7:13 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> Eudes Fileti wrote: >> >> Hello Justin, I am facing a very similar problem to that you >> experienced and described in >> >> (http://www.gromacs.org/pipermail/gmx-users/2008-February/032429.html). >> >> I throw this question in the GMX forum and Berk has kindly >> helped me. But reading the forum I realized that you already >> could be solved the problem so that maybe I could help more >> directly. >> >> >> Please keep Gromacs-related discussions on the list. If you had >> followed the rest of the thread you reference, you will find that my >> calculations were falling victim to a bug in Gromacs-3.3.1. If you >> are using a newer version, then my situation is not applicable, >> since the problem has been fixed (IIRC) as of Gromacs-3.3.3. >> >> If you are using version 3.3.1, re-run your simulations with a newer >> version. >> >> >> I have tried to calculate the free energy of transfer from >> benzene to ethanol >> for a polyhydroxylated (24 OH's). This system has 24 hydroxyl >> groups, and in ethanol, there should be more than 20 >> solute-solvent hydrogen bonds being erased simultaneously (not >> to mention the possible intramolecular HB's). >> >> The Dg/dlambda plot, for both, benzene and ethanol shows a very >> high and narrow peak near lambda=0. In the case of ethanol is >> worse due to the solute-solvent hydrogen bonds. >> I performed two sets of simulations, one for sc-power=1 and >> another for sc-power=2, using the following protocol: >> >> 1) I made disappear the electrostatic interactions turning off >> the charges (by 200ps), 2) At the sequence I made disappear the >> LJ interactions (for more 200ps) 3) Finally I performed a run of >> 0.5ns. >> Correct me i this procedure is inappropriate. >> >> To start, Berk said me that the use of sc-power=2 never is >> recommended. Ok! >> Secondly, then he gave me a good tip that I was not taking into >> account: >> Disappear the electrostatic interactions using hard-core instead >> soft-core. >> I did this and actually work (only in part). >> >> When I used softcore to desappear the electrostatic interations, >> the value of dg/dlambda for lambda = 0 was ~160000. Following >> the tip of Berk, wiht hardcore I got ~2000! >> >> >> Right, you should only need soft-core for the LJ component. >> >> >> However when I needed to use softcore again, now to remove the >> LJ interactions, the value returned back to ~160000.` >> >> >> I don't understand what you mean. Is the total area under the curve >> 160000? That is ridiculously high. >> >> I don't know that I have the expertise to help you much more. I am >> not entirely familiar with your methodology. What I have done in my >> own work is run 21 independent simulations at lambda points between >> 0 and 1 (5 ns each after equilibration), and integrated the >> resulting curve. None of my dV/dl points ever approached that >> magnitude, but I can't comment on your specific case, because I >> don't know what you're doing. >> >> -Justin >> >> >> Could you gimme some insigths to solve this problem? >> Best >> eef >> >> P.S.: You can solve your problem of polyphenolic compound? >> >> _______________________________________ >> 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/ >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? 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