Re: [gmx-users] Coarse-grained Protein-ligand simulations

On 3/29/19 9:17 AM, Mac Kevin Braza wrote: Thank you Professor Lemkul, But would you suggest on how can I coarse-grained the ligand I am using? I have been searching resources online but they do not work in our part. I don't work with CG simulations, so I'm not much help. I would think

Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

On 3/29/19 12:23 PM, Kruse, Luke E.(MU-Student) wrote: Thank you all for the help! Introducing the h-bond constraints into the minimization as well, did reduce the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps but did not remove the problem entirely. I am also

Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

Thank you all for the help! Introducing the h-bond constraints into the minimization as well, did reduce the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps but did not remove the problem entirely. I am also using different coulombtype's in the minimization (Cut-off)

Re: [gmx-users] PME constant shifts.

Great! So I just have to discount this term to obtain the positive energy expected. Thank you very much! Sergio On Fri, Mar 29, 2019 at 4:11 PM Berk Hess wrote: > I mean the q_tot^2 term. > This attractative term goes with the square of the total charge, so has > larger magnitude for AB than

Re: [gmx-users] PME constant shifts.

I mean the q_tot^2 term. This attractative term goes with the square of the total charge, so has larger magnitude for AB than A+B, so the result in negative. Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Sergio Perez Sent: Friday,

Re: [gmx-users] PME constant shifts.

Hello, Thanks for the quick reply, I am not sure if you are referring to this term of the Ewald Sum: V_0 = ( f*beta ) * SUM(q_i^2) / sqrt(pi) Since the sum of the square of the charges of the system (AB) is the same as the sum of the square of the charges of the system (A) plus the same from

Re: [gmx-users] Coarse-grained Protein-ligand simulations

Thank you Professor Lemkul, But would you suggest on how can I coarse-grained the ligand I am using? I have been searching resources online but they do not work in our part. I hope you can help us. Thank you Prof. Lemkul! Best regards, Mac Kevin E. Braza On Fri, Mar 29, 2019, 8:59 PM Justin

[gmx-users] Help needed in using gmx select

Dear Gromacs Developers and Users, I need a small help in GROMACS trajectory analysis. I want to define a selection i.e., 4Ang volume around two residues (from different chains X and chain Y ) that make your binding site --- Within this selection I want count number of waters molecules along

Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

On 3/29/19 4:30 AM, Mark Abraham wrote: Hi, Off topic for this discussion, but what would people think if we changed things around so that grompp would do that constraining, before writing the tpr file? This will mean that the configuration in the tpr does not always match the configuration

Re: [gmx-users] Coarse-grained Protein-ligand simulations

On 3/29/19 3:32 AM, Mac Kevin Braza wrote: Hello everyone, I am simulating a coarse-grained model of a membrane protein (GPCR) in lipid bilayer and an all-atom ligand octopamine. I build the protein, solutes, and membrane in the web server CHARMM-GUI. While, I added the ligand to the protein

Re: [gmx-users] PME constant shifts. (Sergio Perez)

Dear Sergio, If you're using PME, you need to also include the reciprocal contribution. Gerrit Dear gmx comunity, I am trying to calculate the electrostatic interaction of my system for force field development. My system consists of 7 positively charged particles interacting (system A)

[gmx-users] CG lipid diffusion coefficient

Hi all, I ran some CG simulations of a protein inserted in a lipid bilayer, with several lipids. I used the msd tool to compute the lipid (using the PO4) diffusion coefficient. For one of the lipid I got D = 0.6 x 10^-5 cm^2/s, which is 600 um^2/s. According to the Martini website "To

Re: [gmx-users] PME constant shifts.

Hi, The negative energy is due to the uniform background charge that appears when your system has a net charge, not due to shifting of pair interactions. Computing the absolute energy of a periodic system with net charge is meaningless. Cheers, Berk From:

Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi, The standard output of the first set of runs is also something I was interested in, but I've found the equivalent in the complex/TESTDIR/mdrun.out files. What I see in the regresiontests output is that the forces/energies results are simply not correct; some tests simply crash after 1-2

[gmx-users] PME constant shifts.

Dear gmx comunity, I am trying to calculate the electrostatic interaction of my system for force field development. My system consists of 7 positively charged particles interacting (system A) with another positively charged particle (system B). I calculate the electrostatic interaction by doing

Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

Hi, Off topic for this discussion, but what would people think if we changed things around so that grompp would do that constraining, before writing the tpr file? This will mean that the configuration in the tpr does not always match the configuration that was given to grompp, but instead

Re: [gmx-users] Coarse-grained Protein-ligand simulations

Hello everyone, I am simulating a coarse-grained model of a membrane protein (GPCR) in lipid bilayer and an all-atom ligand octopamine. I build the protein, solutes, and membrane in the web server CHARMM-GUI. While, I added the ligand to the protein complex manually using the same coordinates of