[gmx-users] Center on bilayer

I realize this has been discussed at length before, but I can't for the life of me get it to work. I have a system where I want to assemble a bilayer from randomly placed lipids (using charmm36 that is not the main point). After about 50 ns I have what seems to be two (rough) leaflets being

Re: [gmx-users] Liquid-liquid interface and electric field

Tank you for the comment on the parameters. The system is neutral. I do no think that the problem is the energy barrier because in that case the ions would be blocked at the interface but they would at least move in the direction imposed by the field (and not randomly move in their respective

[gmx-users] molecule parameterization in charmm36 using GAAMP server

Dear Gromacs users, I used GAAMP server to get the parameters for a small molecule (this is part of a larger molecule). This server optimizes the charges and all the soft dihedrals in an iteration way (consistent with charmm36 and CGenFF philosophy). The output files also include modified angle,

Re: [gmx-users] MD simulations of two chains protein

*Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Wed, Nov 16, 2016 at 9:15 AM, Khadija Amine wrote: > Hi Mark, > > Below, the link to the rmsf plot I had for my protein throughout 20 ns > simulation. > >

[gmx-users] Regarding trjconv

Dear All, I had one doubt regarding g_trjconv which I used to center my protein after simulation. I got different diffusion values when I used the .xtc file before and after applying trjconv. Which one should be used? Is trjconv just for visualisation or is necessary for analysis too? Does it

Re: [gmx-users] Atomtype SDMSO not found - GROMACS

Thanks a lot everyone. I changed SDMSO to SDmso and it worked :) On Wed, Nov 16, 2016 at 7:50 AM, Justin Lemkul wrote: > > > On 11/15/16 5:22 AM, Manasa Surakala wrote: > >> I am new to GROMACS, running protein-ligand simulation. >> >> The error is as follows: >> >> *Fatal

Re: [gmx-users] molecule parameterization in charmm36 using GAAMP server

On 17/11/16 01:24, Mohsen Ramezanpour wrote: Dear Gromacs users, I used GAAMP server to get the parameters for a small molecule (this is part of a larger molecule). This server optimizes the charges and all the soft dihedrals in an iteration way (consistent with charmm36 and CGenFF philosophy).

[gmx-users] g_energy error

Dear list, I want to investigate the trend of the potential energy of the protein in my system with water. I run : trjconv -f md.trr -o protein.xtc tpbconv -s topol.tpr -o protein.tpr mdrun -rerun protein.xtc -s protein.tpr I got the following errors: WARNING: there may be something wrong with

Re: [gmx-users] Question about decomposition of Lennard-Jones contributions in free energy calculations with Gromacs

On 11/11/16 01:22, Joel Jose Montalvo Acosta wrote: Dear Dr. van der Spoel, Thank for your fast answer. I took time to think and to make tests about why is meaningful to have a dispersion/repulsion decomposition in an alchemical calculation. In general, the solvation free energy (ΔG-solv) can

Re: [gmx-users] Tutorials to apply NMR data on Gromacs calculations of protein struture

Hi Kat, You can do this using Plumed patched onto Gromacs. There's a tutorial for this at https://plumed.github.io/doc-v2.3/user-doc/html/belfast-9.html Best wishes James > Hi All, > > I would like to combine NMR study (specifically relaxation data, RDC and > dihedral restraints) with Gromacs

[gmx-users] Liquid-liquid interface and electric field

Hello everyone, I am trying to simulate an ion transfer at an interface between two immiscible electrolytes solutions. I have prepared a 5x5x5 nm box with the solvents and electrolytes. The system is stable and well equilibrated. The problem now is that when I apply an electric field in the z

Re: [gmx-users] Liquid-liquid interface and electric field

On 16/11/16 09:51, Gschwend Grégoire wrote: Hello everyone, I am trying to simulate an ion transfer at an interface between two immiscible electrolytes solutions. I have prepared a 5x5x5 nm box with the solvents and electrolytes. The system is stable and well equilibrated. The problem now is

[gmx-users] pull code and binding free energy

Dear users, I was trying to do the binding free energy calculation between protein and ligand. I get confused on the preparation of the input files: First question: Why we need to use the pull code in the mdp files for the binding free energy calculation (e.g.the pull code has used in this

Re: [gmx-users] Liquid-liquid interface and electric field

Thank you for yor answer. So, with and without electric field the ions move, sometimes form pairs or separate, etc. Everything looks "normal". The temperature of the box is stable at 300K, and the pressure around 1bar. The size of the box is stable as well. The simulation lasts 2 ns. I think

[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

Thank you Mark: That's a pitty!! I am not an informatician, is for that that I am not trying to implement it, becasue probably I do it not through a good or efficient code. Anyway I've been able to solve my problem using g_select and make_ndx and and very iterative bash scripts on each frame of

Re: [gmx-users] Questions about free energy calculation tutorial

The x-axis of the first figures on the link represents the lambda values for coulombic and van der waals decoupling. First ten values are for Coulombic interactions, last 20 values are for van der waals. So basically I thought to see a minima in this figure at lambda between 18-24 (which is

Re: [gmx-users] Liquid-liquid interface and electric field

On 16/11/16 11:54, Gschwend Grégoire wrote: Thank you for yor answer. So, with and without electric field the ions move, sometimes form pairs or separate, etc. Everything looks "normal". The temperature of the box is stable at 300K, and the pressure around 1bar. The size of the box is stable