Re: [gmx-users] Re: Free energy with Gromacs.
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, 16 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 3. 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 ~16. 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 ~16.` I don't understand what you mean. Is the total area under the curve 16? 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
[gmx-users] Re: Free energy with Gromacs.
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 ~16. 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 ~16.` I don't understand what you mean. Is the total area under the curve 16? 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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@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? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Free energy with Gromacs.
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, 16 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 3. 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 ~16. 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 ~16.` I don't understand what you mean. Is the total area under the curve 16? 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:
