[gmx-users] how to calculate average structure

Dear all; I performed a molecular dynamic simulation(50ns) for a complex aptamer-ligand and I am going to analysis the interaction between aptamer and ligand during the simulation,then I will need the average structure. How can I calculate the average structure, is it correct to use the

Re: [gmx-users] Hydrogen Bond analysis

On 10/4/19 12:11 PM, Pandya, Akash wrote: Hi all, This may sound like a stupid question, but is there a "selection process" within gromacs whereby I can determine the correct donor-acceptor distance and angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing various

[gmx-users] cut in gmx clustsize

Dear all, In clustering what is usually defined as a criteria is a cut-off so that if two atoms or molecules are closer to each other less than the cut-off then those two are being counted to be in a cluster, I see even that in the source code of gmx clustsize where ... /* If distance less than

[gmx-users] Hydrogen Bond analysis

Hi all, This may sound like a stupid question, but is there a "selection process" within gromacs whereby I can determine the correct donor-acceptor distance and angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing various literature that study protein-water/

Re: [gmx-users] Reg: Your suggestions for Gromacs simulation using a cofactor and a Zn ion together

On 10/4/19 7:53 AM, Amit Jaiswal wrote: Hello all, I am a novice in Gromacs and i wanted to do a simulation of a protein-zn-cofactor complex together. The problems raised during simulation are: 1. How can i position restrain Zn ion? You shouldn't apply position restraints to the ion if

Re: [gmx-users] Simulation of membrane associated protein

On 10/4/19 4:52 AM, Olga Press wrote: Prof. Lemkul thank you for your response. I'm using the output file from the charmm gui site after the MD production, which contain an equilibrated DOPC bilayer with TIP3 molecules as the solvent (and I remove the ions before the solvation). I used the

Re: [gmx-users] GROMACS Energy groups

On 10/3/19 10:27 PM, Adip Jhaveri wrote: Hello all, I am simulating a system of two proteins in solution. For the simulation I has specified (in the .mdp file) energygrps as : Protein W_ION. Now in the output energy file, these energy groups are separated only for the Columbic and LJ

Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error

On 10/3/19 8:57 PM, Mijiddorj B wrote: Dear Justin, Thank you very much for your prompt response. Do you mean that I made a mistake when I define the bonds in .rtp file? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor

[gmx-users] Reg: Your suggestions for Gromacs simulation using a cofactor and a Zn ion together

Hello all, I am a novice in Gromacs and i wanted to do a simulation of a protein-zn-cofactor complex together. The problems raised during simulation are: 1. How can i position restrain Zn ion? 2. How can i generate a parameter file for NAD cofactor in Amber forcefield? 3. What are the steps

Re: [gmx-users] Simulation of membrane associated protein

Prof. Lemkul thank you for your response. I'm using the output file from the charmm gui site after the MD production, which contain an equilibrated DOPC bilayer with TIP3 molecules as the solvent (and I remove the ions before the solvation). I used the second option of the gmx_solvate (solvate a

[gmx-users] GROMACS 2018.8 patch release available

Hi GROMACS users, I just released another patch release of GROMACS 2018, bringing the official version to 2018.8! We decided to release this additional patch due to the one big issue that was still present in the 2018 branch that could affect scientific correctness, so we encourage all

Re: [gmx-users] Extracting trajectory

Hi Anupama, I understand your question. But I wonder why do you want all the explicit water molecules within 5 Angstrom of your protein surface? That would be meaningless until and unless you are intending to find the conserved water molecules near the surface of protein. I don't understand your