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.