Re: [gmx-users] Hessian Matrix Doubt

Anirban Ghosh wrote: Hi All, I want to go for Normal Mode Analysis of a protein in water. I have done the energy minimization of the protein with water molecules. But now I want to calculate the Hessian Matrix with only the protein molecules and not the water molecules. Please tell me how to d

[gmx-users] Hessian Matrix Doubt

Hi All, I want to go for Normal Mode Analysis of a protein in water. I have done the energy minimization of the protein with water molecules. But now I want to calculate the Hessian Matrix with only the protein molecules and not the water molecules. Please tell me how to do that. Is there any op

[gmx-users] How to use g_enemat ?

Dear community, I'm trying to extract an energy matrix from an energy file ( .edr) But, the program g_enemat require -groups optioin with Generic data file (groups.dat). At the help page, there is an example like following: 2 Protein SOL How to define the group files of

Re: [gmx-users] how to create a new molecule?

khaled barakat wrote: Hi I am a new user for gromacs, and I need to know the steps to define a new molecule "not a protein" and add it to the building blocks of gromacs? That's what chapter five of the manual is for. Read the chapters before it, too! Mark

Re: [gmx-users] Does Gromacs record all pairwise energies and forces?

Lee-Ping wrote: Dear community, I'm trying to access the individual pairwise energies and forces in an MD simulation, but from looking at the source code, it looks like the individual pairwise energies and forces exist only in the inner-loops. I've been asking GROMACS to print the forces out to

[gmx-users] how to create a new molecule?

Hi I am a new user for gromacs, and I need to know the steps to define a new molecule "not a protein" and add it to the building blocks of gromacs? thank you looking for your reply khaled Moody friends.

[gmx-users] Does Gromacs record all pairwise energies and forces?

Dear community, I'm trying to access the individual pairwise energies and forces in an MD simulation, but from looking at the source code, it looks like the individual pairwise energies and forces exist only in the inner-loops. I've been asking GROMACS to print the forces out to a file by modifyin

Re: [gmx-users] Free energy calculation

Why not do a steered MD or umbrella sampling, where you start with the ligand in the binding pocket (in its correct conformation) and gradually pull it out. If done correctly, you should get a nice PMF. > Hello! > I need to calculate the free energy of complex formation between protein A > and li

[gmx-users] Free energy calculation

Hello! I need to calculate the free energy of complex formation between protein A and ligand B. I am about to simulate in solution the molecular dynamics of A, B and AB complex separately and calculate the free energy of each system using g_lie. Then, I suppose, deltaG = G(AB) - (G(A) + G(B)).

[gmx-users] publishing with development version of Gromacs

Hello, I am running protein simulations in an explicit membrane environment, and have found that the CVS development version of Gromacs works much faster than the released version. Is it okay to publish simulations performed on the development version? What kind of validation would I need if I

Re: [gmx-users] Explanation of contents of md.log file requested

Brian Smith wrote: Greetings, A summary of different energy contributions is written to the the md.log file during an MD calculation. Below is an extract,... Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14LJ (SR) 2.93814e+034.04053e+017.7362

[gmx-users] Explanation of contents of md.log file requested

Greetings, A summary of different energy contributions is written to the the md.log file during an MD calculation. Below is an extract,... Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR) 2.93814e+034.04053e+017.73620e+01 -2.06722e