Re: [gmx-users] Simulation of charged systems (2)
Hi, thanks to Justin for the pointer to the list archive I searched before with net charge, but without getting useful results. For the sake of clarity, I am not referring to the neutralizing plasma or neutralizing background charge used implicitly with PME, but to an additional net-charge correction implemented for example in CHARMM to avoid, at least partly, the artifacts produced by that neutralizing background charge in net-charged systems, which are sometimes unavoidable (s., eg., Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84. http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1). Felipe On 11/05/2012 02:27 PM, Justin Lemkul wrote: On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote: Hi again! many thanks to Xavier for his response, the only one I got so far ... I had the same impression, but I'm seeking for theoretically/technically more funded statements. My impression is also that there are different kind of equations depending of the treatment of long-range electrostatic interactions. My concrete question is now: are net charge corrections to the Ewald potential implemented in Gromacs? http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html Searching the list archive for neutralizing background charge turns up a large number of results. This is a fairly common question, and there are many replies with varying degrees of detail. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of charged systems (2)
Hi again! many thanks to Xavier for his response, the only one I got so far ... I had the same impression, but I'm seeking for theoretically/technically more funded statements. My impression is also that there are different kind of equations depending of the treatment of long-range electrostatic interactions. My concrete question is now: are net charge corrections to the Ewald potential implemented in Gromacs? Thank you and kind regards, Felipe On 11/02/2012 10:54 AM, XAvier Periole wrote: From what I remember from my earlier impressions ... the equations are not correct when the system is not neutral. In your case the charge is significantly high ... On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote: Hi, I recently sent a query, but it was probably not appealing enough to get some feedback. So I try again with a shorter one: Is there any theoretical or technical objection against running an NPgammaT simulation on a charged (total charge = -36) membrane model (hydrated bipolar monolayer) using PME? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of charged systems (2)
On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote: Hi again! many thanks to Xavier for his response, the only one I got so far ... I had the same impression, but I'm seeking for theoretically/technically more funded statements. My impression is also that there are different kind of equations depending of the treatment of long-range electrostatic interactions. My concrete question is now: are net charge corrections to the Ewald potential implemented in Gromacs? http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html Searching the list archive for neutralizing background charge turns up a large number of results. This is a fairly common question, and there are many replies with varying degrees of detail. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of charged systems (2)
From what I remember from my earlier impressions ... the equations are not correct when the system is not neutral. In your case the charge is significantly high ... On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote: Hi, I recently sent a query, but it was probably not appealing enough to get some feedback. So I try again with a shorter one: Is there any theoretical or technical objection against running an NPgammaT simulation on a charged (total charge = -36) membrane model (hydrated bipolar monolayer) using PME? Many tanks in advance for your input. Best, Felipe +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Linnaeus University | | SE-391 82 Kalmar | | Sweden - Sverige | +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulation of charged systems
Dear Colleagues, I am currently carrying out MD simulations on models of archaeal membranes. These membranes, contrary to those of bacteria or eukariota, are made of unconventional lipids. In my case they contain a neutral carbohydrate headgroup and the second one is a negatively charged phospho-myoinositol, contrary to neutral (zwitterionic) phosphocholine found in conventional lipids. In order to have a neutral system to carry out the simulation on: 1. I could add 36 positive counterions (eg, Na+) to my membrane model, which would correspond to approx. 900 mM of these ions for the amount of water molecules I am using. This concentration is of course not only much higher than a physiological one, although it is, strictly speaking, not a salt, i.e. NaCl, concentration. The issue is that I would like to study the effect of salt (alkali cations) on the membrane properties and therefore would need a suitable, possible ion/salt-free system as reference state. 2. I could protonate the phosphate and have -O-P(OOH)-O- instead of -O-P(O2-)-O-. This would provide a neutral, salt-free reference state, but the issue is that this phosphate group would be probably de-protonated in the cellular compartment it is localized, which has a pH of approx 6. Another option would be to run the simulations on the charged system, without counterions, but I am not quite sure if there are technical problems with that. I am using the following settings for the treatment of long-range electrostatics: ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT I wonder if someone could kindly advise me in this issue. Any suggestion or comment will be highly appreciated. Best regards, Felipe +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Linnaeus University | | SE-391 82 Kalmar | | Sweden - Sverige | +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
