Re: [gmx-users] solvent evaporation modeling
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 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 > > >> 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 >> > 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 >> >> 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 > >
Re: [gmx-users] solvent evaporation modeling
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 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 > 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 > > 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 > >> 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 > >>> 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
Re: [gmx-users] solvent evaporation modeling
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 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 > 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 >> 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 >>> 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 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 >
Re: [gmx-users] solvent evaporation modeling
Den 2019-12-02 kl. 00:03, skrev SAKO MIRZAIE: 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 Alexandra Patriksson, Erik Marklund and David van der Spoel: Proteins Structures under Electrospray Conditions Biochemistry 46 pp. 933-945 (2007) Yaofeng Wang, Daniel Larsson and David van der Spoel: Encapsulation of Myoglobin in a CTAB micelle - A Simulation Study Biochemistry 48 pp. 1006-1015 (2009) Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel & Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) Friemann, Rosmarie; Larsson, Daniel; Wang, Yaofeng; Van der Spoel, David: Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in vacuo J. Amer. Chem. Soc. 131 pp. 16606-16607 (2009) And a review in David van der Spoel, Erik G. Marklund, Daniel S. D. Larsson and Carl Caleman: Proteins, Lipids and Water in the Gas Phase Macromolecular Bioscience 11 pp. 50-59 (2011) -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
Re: [gmx-users] solvent evaporation modeling
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 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 > 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 >> 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 >>> 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=viwZvVAJ=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.
Re: [gmx-users] solvent evaporation modeling
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 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 > 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=viwZvVAJ=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.
Re: [gmx-users] solvent evaporation modeling
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 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 -- 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.
[gmx-users] solvent evaporation modeling
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.
