Dear Anders and Kalil, Thank you for your answers and for sharing the scripts. I will help a lot.
Best, On Tue, Dec 3, 2019 at 5:12 PM Anders Støttrup Larsen <anders...@gmail.com> wrote: > Hi Sako > > I did something similar where I dehydrated a system of water molecules, in > my case a crystal but the principles are the same. > > I have uploaded the script at > > https://github.com/aslarsen/gromacs_dehydration/blob/master/gromacs_dehydration_MPI_V2.py > > It was used in this paper > https://pubs.acs.org/doi/abs/10.1021/acs.cgd.7b00889 > > I used gromacs 5.1.4 so you might have to update it to your version and > set whatever parameters you want. > > Best Wishes > Anders > > On Tue, Dec 3, 2019 at 10:36 PM Kalil Bernardino < > kalil.bernard...@gmail.com> wrote: > >> Dear Sako, >> >> >> Unfortunately I don't have access to the script in the present since I'm >> in >> the middle of a travel. But anyway it was done in a specific way for the >> system that we were working on that time and would need some changes to >> work with different systems. >> >> I can describe to you the general idea here. >> >> >> First, there is two ways to simulate the solvent evaporation and we >> performed both in the paper André cited. The more physical way, since we >> were working with a liquid vacuum interface, suppose perpendicular to z >> direction, was to run a short simulation, save the final structure, check >> which molecules are above some zcut value, exclude they from your >> structure, rewrite the topology file to update the number of molecules, >> run >> the grompp to produce the new tpr and run a new short simulation. This >> would be something similar to have a liquid with a vacuum pump at z = >> zcut, >> and any molecule that enters the vacuum pump will be removed from the >> system. For this protocol, you should work with constant volume >> simulations. >> >> >> The problem with this procedure is that it can be very slow, specially >> when >> you have too few solvent remaining or if your system have a small vapor >> pressure, as is your case since you are working with water. So, if you >> want >> to complete dry your system, you can remove molecules randomly in the >> following way. You may or may not want to create a liquid/vacuum >> interface, >> depending if you want to simulate the molecule in some interface or if you >> want to simulate the bulk of something that in being dried. If you have a >> vacuum interface, you need to work with NVT simulations, but in order to >> make a bulk simulation you should do in a NPT ensemble. >> >> >> 1- Equilibrate your system with the solvent >> >> 2- Save the final structure >> >> 3- Delete some fraction of randomly selected solvent molecules. You can do >> this directly with some script or can use the gromacs command genion to >> randomly convert some molecules in some monoatomic specie (for instance, >> "genion -np 60 -pname DEL" and select the water for replace 60 water >> molecules with 60 particles with name DEL), make_ndx to generate a index >> file with a group including every molecules except the specie produced by >> genion (DEL in the example) and then the editconf reading the index.ndx in >> order to produce a new .gro file with every molecule except the deleted >> ones. This .gro will be your initial structure for next step. If you want >> to use the gromacs commands for this remotion, remember to run the grompp >> again from your final structure to produce a new tpr file before using >> genion. >> >> 4- Rewrite your topology file in order to update the number of solvent >> molecules >> >> 5- Run grompp and mdrun to do a short simulation with this small numer of >> water molecules and save the final structure >> >> 6- If still have water in your system (or if have more water than you want >> in your final structure), go back to step 3 and continue removing. >> >> >> You should not remove a large amount of molecules in a single step or this >> can lead to some artificial structures. And by the end of your process, >> when you have only a small amount of solvent, I think it is better to >> reduce even more the amount removed at each step (which is not so bad >> because your simulation will run faster at this point). >> >> >> Hope this protocol helps you. >> >> >> Best, >> >> Kalil >> >> >> >> Em seg., 2 de dez. de 2019 às 14:14, SAKO MIRZAIE <sako.bioc...@gmail.com >> > >> escreveu: >> >> > Dear André, >> > >> > Thank you very much for your email and hope Kalil has the script. >> > >> > Best regards >> > >> > On Mon, Dec 2, 2019 at 7:15 AM André Farias de Moura <mo...@ufscar.br> >> > wrote: >> > >> >> Dear Sako, >> >> >> >> I'm ccing Kalil, who actually wrote and run the script to remove >> solvent >> >> molecules, he might still have it. >> >> >> >> regards >> >> >> >> Andre >> >> >> >> On Mon, Dec 2, 2019 at 2:54 AM SAKO MIRZAIE <sako.bioc...@gmail.com> >> >> wrote: >> >> >> >>> Dear André, >> >>> >> >>> Thank you for your response. >> >>> Could you send me such a script? >> >>> >> >>> On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura <mo...@ufscar.br >> > >> >>> wrote: >> >>> >> >>>> Dear Sako, >> >>>> >> >>>> we did something like that a few years ago, please take a look at >> DOI 10.1039/C4CP03519D >> >>>> for details. >> >>>> >> >>>> in a nutshell: you need a script that runs a sequence of short >> >>>> equilibration and production runs after a number of solvent >> molecules are >> >>>> removed (implying that topology needs to be updated for the number of >> >>>> solvent molecules at each round, so the script needs to include some >> >>>> parsing of the files as well). >> >>>> >> >>>> Andre >> >>>> >> >>>> On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE <sako.bioc...@gmail.com> >> >>>> wrote: >> >>>> >> >>>>> Hi All, >> >>>>> >> >>>>> I want to simulate a polymer: protein system in a way that water >> >>>>> solvent >> >>>>> will evaporated gradually. How should I do that? What parameters are >> >>>>> needed >> >>>>> to be included in the mdp file. >> >>>>> >> >>>>> Best >> >>>>> >> >>>>> >> >>>>> >> >>>>> -- >> >>>>> *********************************************** >> >>>>> Sako >> >>>>> -- >> >>>>> Gromacs Users mailing list >> >>>>> >> >>>>> * Please search the archive at >> >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >>>>> posting! >> >>>>> >> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>>>> >> >>>>> * For (un)subscribe requests visit >> >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> >>>>> send a mail to gmx-users-requ...@gromacs.org. >> >>>>> >> >>>> >> >>>> >> >>>> -- >> >>>> _____________ >> >>>> >> >>>> Prof. Dr. André Farias de Moura >> >>>> Department of Chemistry >> >>>> Federal University of São Carlos >> >>>> São Carlos - Brazil >> >>>> phone: +55-16-3351-8090 >> >>>> >> >>> >> >>> >> >>> -- >> >>> *********************************************** >> >>> Sako Mirzaie >> >>> Sako Mirzaie >> >>> Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic >> >>> Azad University of Sanandaj, Sanandaj, Iran >> >>> >> >>> Visiting Professor, Advanced Pharmaceutics >> >>> >> >>> & Drug Delivery Laboratory >> >>> >> >>> Leslie Dan Faculty of Pharmacy >> >>> >> >>> University of Toronto >> >>> >> >>> 144 College Street, Toronto, Ontario >> >>> >> >>> Canada M5S 3M2 >> >>> >> >>> http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en >> >>> >> >>> http://www.scopus.com/authid/detail.url?authorId=54886431500 >> >>> >> >>> http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie >> >>> https://www.researchgate.net/profile/Sako_Mirzaie/publications/ >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >> >> >> -- >> >> _____________ >> >> >> >> Prof. Dr. André Farias de Moura >> >> Department of Chemistry >> >> Federal University of São Carlos >> >> São Carlos - Brazil >> >> phone: +55-16-3351-8090 >> >> >> > >> > >> > -- >> > *********************************************** >> > Sako Mirzaie >> > >> > >> > >> > >> > >> > >> > >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > -- *********************************************** Sako Mirzaie Sako Mirzaie Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad University of Sanandaj, Sanandaj, Iran Visiting Professor, Advanced Pharmaceutics & Drug Delivery Laboratory Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street, Toronto, Ontario Canada M5S 3M2 http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en http://www.scopus.com/authid/detail.url?authorId=54886431500 http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie https://www.researchgate.net/profile/Sako_Mirzaie/publications/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.