> 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? Thank You Regards Zaved > A lot of OPs have the tendency to follow-up with private emails and I feel > it should stay public so other people might benefit from the information > as > well. Here is the rest of the conversation regarding this thread. > > """ > Dear Zaved, > > I'm not aware of any tutorials for Gromacs, and Gromacs does not support > constant-pH MD simulations straight out of the box. It must be (heavily) > modified. Amber comes pre-packaged with constant-pH functionality, I > believe. Still, you probably don't want to get involved in any of this. My > comment about it was merely to make you aware that changing the > protonation > states by hand doesn't make mean you're really simulating at a given pH. > Still, 99.9% of the people in this field do what you were wanting to do, > i.e., change the protonation states during pdb2gmx to whatever they feel > is > more representative of that residue at a given pH and then hit run. I also > do it, unless I'm studying something where charge regulation playes a > major > role, so by all means go ahead and try the simpler solution first. > > P.S.: Please avoid sending private messages about these subjects. It > started in gmx-users and should stay there for several reasons. The main > one is that other people might have the same problem and this information > might be useful for them as well. > > Best regards, > J > > On Tue, Jan 16, 2018 at 6:54 AM, <za...@tezu.ernet.in> wrote: > >> Dear Sir >> >> Thank you for your kind response regarding the -inter command. >> >> Sir can you guide / provide any tutorial for constant-pH MD simulation >> in >> gromacs (eg., to perform simulation at pH 9)? >> >> I shall be grateful to you for the same. >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> Napam, 784028, >> Assam, >> India >> >> >> * * * D I S C L A I M E R * * * >> This e-mail may contain privileged information and is intended solely >> for >> the individual named. If you are not the named addressee you should not >> disseminate, distribute or copy this e-mail. Please notify the sender >> immediately by e-mail if you have received this e-mail in error and >> destroy >> it from your system. Though considerable effort has been made to deliver >> error free e-mail messages but it can not be guaranteed to be secure or >> error-free as information could be intercepted, corrupted, lost, >> destroyed, >> delayed, or may contain viruses. The recipient must verify the integrity >> of >> this e-mail message. > > """ > > J > > On Mon, Jan 15, 2018 at 11:51 AM, Jo?o Henriques < > joao.m.a.henriq...@gmail.com> wrote: > >> -inter sets the interactive mode for a bunch of other flags. Most are >> used >> for selecting the protonation states of the termini and other residues. >> It >> can also be used for interactive SS bridge selection. >> >> > "for setting the protonation state of charged amino acids in order to >> perform simulation at different pH?" >> >> Please note that changing the protonation states of the residues does >> not >> mean you're performing the simulation at a "different pH". A proper >> constant-pH MD simulation allows the residues to titrate in respect to >> the >> solution pH as well as the their "molecular environment". In this case, >> your residues will be "stuck" in a user defined protonation state that >> may >> or may not reflect the most populated protonation states of those >> residues >> at a given pH, irrespectively of their surroundings. >> >> Cheers, >> J >> >> On Mon, Jan 15, 2018 at 11:00 AM, <za...@tezu.ernet.in> wrote: >> >>> Dear Gromacs Users >>> >>> I have an query regarding gmx pdb2gmx -inter command. >>> >>> Do we use -inter command only for setting the protonation state of >>> charged >>> amino acids in order to perform simulation at different pH? >>> >>> >>> Thank You >>> >>> Regards >>> Zaved Hazarika >>> Research Scholar >>> Dept. Of Molecular Biology and Biotechnology, >>> Tezpur University, >>> India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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.
