Re: [gmx-users] non-neutral system

Hi, The negative Coulomb energy is due to the interaction of your positively charged Argon atoms with the background charge of +10. However, I nevertheless expect that the dynamics will be that of all atoms repelling, as the uniform background charge does not exert a force in your case. Also,

Re: [gmx-users] non-neutral system

Hi Justin, I have a system of 500 Argon fluid each given a charge +0.20 (vdW cut-off=0.8 nm). So I expect the system to have total positive coulomb potential (repulsion). Below are simualtion results of PME and cut-off: PME coulomb results: Energy Average Err.Est.

Re: [gmx-users] non-neutral system

Understood. Thank you Justin. J On Mon, Nov 6, 2017 at 1:11 PM, Justin Lemkul wrote: > > > On 11/6/17 7:06 AM, João Henriques wrote: > >> Hi Johannes, >> >> I just meant that from a purely theoretical point of view, it needs to be >> neutral. This has to do with the

Re: [gmx-users] non-neutral system

On 11/6/17 7:06 AM, João Henriques wrote: Hi Johannes, I just meant that from a purely theoretical point of view, it needs to be neutral. This has to do with the convergence of the outer infinite series, as the paper Micholas linked clearly states. I sincerely hope I'm not botching this up,

Re: [gmx-users] non-neutral system

Hi Johannes, I just meant that from a purely theoretical point of view, it needs to be neutral. This has to do with the convergence of the outer infinite series, as the paper Micholas linked clearly states. I sincerely hope I'm not botching this up, but this is the conclusion I've withdrawn from

Re: [gmx-users] non-neutral system

In the link it says: "Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net

Re: [gmx-users] non-neutral system

On 11/6/17 5:50 AM, Faezeh Pousaneh wrote: Hi, I have a system containing similar charged atoms. So the total charge is not zero. Simulation results with cut-off coulomb seems reasonable, but using PME they are wrong (total columb potential is negative value which must be positive). Any

Re: [gmx-users] non-neutral system

On 11/6/17 6:03 AM, Hermann, Johannes wrote: Hey Joao, are you sure? I think PME will introduce a neutralizing background charge? It does. Whether or not it's appropriate is another matter. For homogeneous systems, it's fine, but if dealing with something heterogeneous like a membrane,

Re: [gmx-users] non-neutral system

Thank you guys. Johanns, I think one must add counter-ions by himself (which I do not want), as written here http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge Best regards On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes < j.herm...@lrz.tu-muenchen.de> wrote:

Re: [gmx-users] non-neutral system

Hey Joao, are you sure? I think PME will introduce a neutralizing background charge? All the best Johannes On 06.11.2017 11:57, João Henriques wrote: ​Hi, You shouldn't use PME without neutralizing the system's charge. ​It's a limitation of the Ewald summation. Take a look at the

Re: [gmx-users] non-neutral system

Faezeh Pousaneh <fpoosa...@gmail.com> Sent: Monday, November 06, 2017 5:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] non-neutral system Hi, I have a system containing similar charged atoms. So the total charge is not zero. Simulation results with cut-off c

Re: [gmx-users] non-neutral system

​Hi, You shouldn't use PME without neutralizing the system's charge. ​It's a limitation of the Ewald summation. Take a look at the literature for further details. I don't know much about viscosity, so I'll leave that for someone else. Cheers, J On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh

[gmx-users] non-neutral system

Hi, I have a system containing similar charged atoms. So the total charge is not zero. Simulation results with cut-off coulomb seems reasonable, but using PME they are wrong (total columb potential is negative value which must be positive). Any idea why? If I use counter-ions to neutralize

Re: [gmx-users] Non-neutral system with iron-sulfur clusters

On 6/14/16 7:37 AM, Marlon Sidore wrote: I checked everything and even by adding the numbers on the paper and the cystein charges from amber03 (the FF they used in the paper) the resulting charge isn't an integer. The paper has charges for the Fe (4x), the S (4x) from the cluster, the S from

Re: [gmx-users] Non-neutral system with iron-sulfur clusters

I checked everything and even by adding the numbers on the paper and the cystein charges from amber03 (the FF they used in the paper) the resulting charge isn't an integer. The paper has charges for the Fe (4x), the S (4x) from the cluster, the S from the CYS bound to it and the CB bound to the

Re: [gmx-users] Non-neutral system with iron-sulfur clusters

On 6/14/16 4:59 AM, Marlon Sidore wrote: Hello everyone, On my quest to use the parameters for iron-sulfur clusters from [1] I realized that the resulting clusters are not neutral. Indeed, even though the charges of the 2 CYS atom (SG and CB) are modified, the overall charge of the cluster +

[gmx-users] Non-neutral system with iron-sulfur clusters

Hello everyone, On my quest to use the parameters for iron-sulfur clusters from [1] I realized that the resulting clusters are not neutral. Indeed, even though the charges of the 2 CYS atom (SG and CB) are modified, the overall charge of the cluster + the 4 CYS isn't a round number. Should I

[gmx-users] Non-neutral system

Dear All users, I want to simulate a non-neutral system including cations with gromacs. It can be possible? I want to use Ewald summation for long for calculating range range interactions. I see in Error page of gromacs: Note for PME users: It is possible to use a uniform neutralizing

Re: [gmx-users] Non-neutral system

Hi, technically, you can use PME with charged systems in Gromacs. However, if the charges in your system are distributed inhomogeneously (as, e.g. in a water/membrane system), you will get artefacts, as described in http://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf Best, Carsten On 23 Apr

Re: [gmx-users] Non-neutral system

Dear Carsten, Thank you very much for your reply. Yes, it is distributed inhomogeneously. In fact I want to investigate the solvation energy of cations in water(12 cations, total charge +24e). Initial configuration includes cations near the surface of water and then they should diffuse into the