[gmx-users] binding energy

Dear all,I am using umbrella sampling tutorial (Justin tutorial). I just wondering the binding energy is Gibbs free energy or Helmholtz free energy?and how can I find the difference between these two free energies? Thanks,Negar -- Gromacs Users mailing list * Please search the archive at

[gmx-users] wham analysis

Dear all, I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for wham

[gmx-users] wham analysis

Dear all, I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for wham

[gmx-users] wham analysis

 Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for

[gmx-users] Wham analysis

Dear all, I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for wham

[gmx-users] umberlla sampling of protein ligand complex

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said:

[gmx-users] (no subject)

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said:

[gmx-users] umberlla sampling of protein ligand complex

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said:

[gmx-users] Removing water

Dear all users, I am using tutorial Kalp15 in DPPC from Justin's tutorials.I want to remove waters which are between bilayers so I use this script: http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations #!/bin/bash # give x.gro as first command line arguement upperz=6.417

[gmx-users] Prolactin receptor in a mixed DPPC-DMPC bilayer

Dear all Gromacs users, I want to simulate prolactin receptor in a mixed DPPC-DMPC bilayer. At first, I will insert the trans membrane part of the protein (prolactin receptor) in the bilayer and do the necessary modifications to the FF, according to the Justin,s membrane protein tutorial. It

[gmx-users] KALP 15 in model membrane

Dear all Gromacs usersI have started the tutorial on membrane protein, provided by Justin ( KALP 15 in model membrane).Now I have two questions:1) Why Justin adds the ACE and NH2 groups to the two ends of the peptide model? The -ter option in pdb2 gmx command can add interactively the NH2 or

[gmx-users] simulation of water

Dear all users, I am new to Gromacs and I want to simulate a box of pure water.I want to know is there any tutorial for this simulation with Gromacs? or Could anyone kindly help me? Thanks in advance,Negar -- Gromacs Users mailing list * Please search the archive at

[gmx-users] 4096 characters

Dear all users, I have a question about characters.I want to simulate protein-ligand complex from Justin Lmkul tutorial .When I run this line:gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0I get this error:"Fatal error:An input file contains a line longer than 4096 characters

[gmx-users] linux or windows

Dear all users, I want to install gromacs on my PC, but I don't know which operating system is better: linux or windows and it is important that doesn't loose capabilities of the software? In any case, which version of operating system is better for installation? Thanks in advance,Negar --

[gmx-users] membrane proteins simulation

Dear all users, I am new in membrane proteins simulation. I want to simulate a membrane protein that it is a part of a large protein and has a big extracellular part.Here is my question: is it ok, I just simulate the membrane part even it is a part of a large protein? and if the answer is

[gmx-users] docking

Hello friends, I want to dock a simulated protein like: human serum albumin to the drug. I was wondering if i could use docking with gromacs or other softwares?If I can use gromacs docking, where can i find a good tutorial ? thank you,Negar.Parvizi -- Gromacs Users mailing list * Please search

[gmx-users] Gromacs error regarding default gromos bond type and angle type

Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the

[gmx-users] Fw: Gromacs error regarding default gromos bond type and angle type

Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the

[gmx-users] Interuption Simulation

Dear Gromacs users I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report

[gmx-users] Interuption Simulation

Dear Gromacs users I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report

[gmx-users] interrupt simulation

Dear Gromacs users I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report

[gmx-users] .rtp files

Dear Gromacs users; I use Gromacs version 4.5.4. I finished protein-ligand complex tutorial(Dr.justin lemkul tutorial). Now i want to use my ligand. I am new in this field(charge group blocking). For getting an idea about charge group blocking, i check .rtp files. cheking aminoacides.rtp files

[gmx-users] GROMOS96 user guide

Dear Gromacs Users, Does anyone know where i can get 'GROMOS96 manual and user guide'(van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf

[gmx-users] charge groups

would be greatly appreciated. N.P On Sunday, June 8, 2014 11:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/8/14, 2:34 PM, Negar Parvizi wrote: Dear Gromacs Users, Does anyone know, where can i find information about Gromos96 building blocks for suitable chargegroupings? Look

[gmx-users] charge groups

Dear Gromacs Users, Does anyone know, where can i find information about Gromos96 building blocks for suitable chargegroupings? Thanks in advance, N.P -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Fw: charge groups

On Sunday, June 8, 2014 11:04 PM, Negar Parvizi negar.parv...@yahoo.com wrote: Dear Gromacs Users, Does anyone know, where i can find information about Gromos96 building blocks for suitable chargegroupings? Thanks in advance, N.P -- Gromacs Users mailing list * Please search

[gmx-users] Simulation of wild and mutant types of HSA protein

Dear Gromacs users I have a question about protein simulation in Gromacs. We are interested in the effect of single point mutation on the structure of HSA (human serum albumin) protein. We selected a pdb file for wild type HSA and submitted it for MD simulation. One of the mutatns of HSA is