On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote:
Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: -inter command (Jo?o Henriques) 2. Rupture force definition (Rakesh Mishra) 3. Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Jan 2018 08:30:10 +0100 From: Jo?o Henriques <joao.m.a.henriq...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -inter command Message-ID: <CAHv45qOCV7fOu8heK0q1w_=gdzmevrcxz35ct8xxzfwwngu...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8"Thank you so much Joao Sir for your kind response. 1. I have predicted the pka values for my protein using H++ server. 2. Based on the pka values, I have set the protonation states of the charged residues using -inter command for pH 9. 3.I have run my simulation at pH 9 (keeping charge of +8e) using gromacs 5.1.4 and gromos54a7 ff. After performing 100ns simulation, I didn't observed any change compared to control system. Can you provide any advice on it?
In what ways do the "pH 9" and "control" simulations differ? What do you define as "control" in this instance, default protonation by pdb2gmx? If that's the case, unless you have some very noncanonical pKa values, there's nothing that's really expected to be different between these two pH values, except perhaps the N-terminus itself.
What are you trying to compare or calculate? Perhaps 100 ns is insufficient to observe whatever it is you're after. How have you quantified that there is no difference/change between these systems?
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
