Dear Justin, Thank you very much. I will try the possible water models.
Do you know if there are water models to resemble frozen state? Yours sincerely Cheng ------------------ Original ------------------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng ------------------ Original ------------------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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.
