Re: [gmx-users] Fwd: Lysosyme in water

gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic Try the above command On Mon, 5 Jun 2017 at 10:16 AM, shivanigupta.gup...@gmail.com < shivanigupta.gup...@gmail.com> wrote: > Dear Gromacs > > I am new and a beginner to this system. I am trying to learn through >

[gmx-users] Fwd: Lysosyme in water

Dear Gromacs I am new and a beginner to this system. I am trying to learn through tutorials for version 5. When i performed i got the following error . [shivani@POLY3 tut1]$ editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic -bash: editconf: command not found [shivani@POLY3

[gmx-users] Fwd: tetrahedral order parameter

-- Forwarded message -- From: ISHRAT JAHAN Date: Fri, Jun 2, 2017 at 10:29 AM Subject: Re: [gmx-users] tetrahedral order parameter To: gmx-us...@gromacs.org I have used gmx hydorder but unable to understand the output as it gives two .xpm and two .out file.

[gmx-users] QM/MM with Orca

Hi all, I have managed to compile Gromacs (2016 and 5.0.7) and run a simple QM/MM calculation with Orca as the QM engine, a MD run for a small peptide in vacuum. (If anyone is interested, I can share the procedure, adapted from a tutorial I found on the web.) However, the question I have is not

Re: [gmx-users] RMSD Matrix error

Hi, On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand wrote: > Dear All, > > When I'm trying to construct a RMSD matrix , using the command > g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m > rmsd-matrix.xpm -tu ns > > I get the error: > Last frame

[gmx-users] Negative deuterium order parameters

Hello: I made 5 simulation: pure DPPC+a molecule inside, pure DPPE+molecule inside, 50% DPPC-50% DPPE+molecule inside, 75% DPPC-25%DPPE+molecule inside and 25%DPPC-75% DPPE+molecule inside. All the graphics were fine, but when i plot my system with 25%DPPC-755DPPE+Molecule inside the graphic

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Hi, Further, I would measure the distribution of the lifetime of hydrogen bonds, since you need to sample much longer than eg the average. And you should also try to measure the autocorrelation time of the number of hydrogen bonds - you don't have a "new" observation until you've simulated at

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Hi Apramita, you have not told us how many urea molecules you have added to you system, neither have you told how large your peptide of interest is, but usually people studying denaturation of peptides use very concentrated urea solutions (typically 8 M or so), which are highly viscous. If this

[gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

Dear All, I have tested with two ways of solvating a peptide with urea-water mixture Method 1: Pre-equilibrating a urea-water box and solvating the peptide with -cs option with this box Method 2: Adding urea molecules to peptide box using -ci option and then solvating the resulting box with

Re: [gmx-users] EM error

Can anyone please help me? Mohammad From: ‪Mohammad Roostaie‬ ‪ To: "gmx-us...@gromacs.org" Sent: Wednesday, 31 May 2017, 8:27:59 Subject: EM error Hi All, I wanted to run energy minimization process by this command: gmx mdrun -v

[gmx-users] RMSD Matrix error

Dear All, When I'm trying to construct a RMSD matrix , using the command g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m rmsd-matrix.xpm -tu ns I get the error: Last frame 20 time 20.000 Building RMSD matrix, 21x21 elements element 28982; time 2.90 Killed I