>>>>> 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 >> >> Thank you so much Justin. >> >> 1. Yes you are correct. control here means default protonation state and >> in this case the system charge of +8e is neutralized. I didn't have any >> noncanonical pka values (at ph9). Checked with both H++ server and >> Propka. >> For ph 9, I have kept the charge of +8e. >> >> 2. Our experimental data suggests that at higher pH (9), the protein >> initiates unfolding. >> >> 3. I have taken the final structure (at 100ns) of both systems and >> superimposed it. I got a RMSD of 1.030 angstrom and no major structural >> change was observed. >> >> 4. We can consider to extend the simulation to visualize any change, if >> above things are correct. > > There won't be one. Since the topologies are identical, you're running > the same simulation twice, and concluding that there are no major > variations between the two. You don't actually have any simulation that > you can claim is representing anything other than "pH 7," though pH > isn't really a thing in fixed-charge/fixed-topology MD. This is a > limitation of modeling something with fixed protonation states; it > doesn't necessarily reflect reality. A constant pH method might show > some results, but AFAIK this is not possible in GROMACS (though some > people do have custom code in old versions that might work). You may > want to consider a different program like AMBER or CHARMM that can do > these types of simulations. > > -Justin
Thank You so much Justin. Can you provide the name and any link for older gromacs version? Thank You * * * 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.