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Hi all, I had simulate charged polymers and surfaces, and is very common to have interaction of ion bridge (or ionic crosslinking) which consist of and interaction of two equally charged groups...
25 June 2020 1,928 1 View
I want to simulate polyelectrolyte of PPO . I inserted counterions into the simulation box and changed their position near the protonated group with position.dat file. but after minimization and...
20 May 2020 5,756 4 View
Chemshell and orca combined for QM / MM calculation. Atomic number in QM is 34.The total number of atoms is 11900. Frequency calculation shows:ORCA finished by error termination in SCF...
16 May 2020 3,391 0 View
Chemshell and orca combined for QM / MM calculation. Atomic number in QM is 34.The total number of atoms is 11900.Optimizing calculation of triplet state is OK.Frequency calculation shows:ORCA...
12 May 2020 6,536 0 View
I'm trying to apply the continuity and differentiability theorems, shown in the book "Ordinary Differential Equations" from Philip Hartman pages 94 and 95 respectively, Continuity Theorem....
09 May 2020 8,915 0 View
I am currently using gromacs 2020 for my MD simulation (Protein-Ligand) and i have g_MMPBSA 5.1.x installed. after entering the command, g_mmpbsa -f md_0_10_center.xtc -s md_0_10.tpr -n index.ndx...
06 May 2020 4,335 5 View
Hi all I am new to GROMACS and need help with some issues. (1) I am trying to run a simulation for glucose in water. The topology file for glucose was generated using AMBER and GLYCAM_06j-1...
05 May 2020 9,094 2 View
Is it valid to compare the wild type protein against the protein that has been truncated due to stop codon mutation using molecular dynamics simulations?
04 May 2020 1,956 3 View
I can calculate the height of parabola based on angular velocity and radius but the problem become complex as this rotating cylinder has various holes on top half of its circumference. Also, the...
03 May 2020 8,719 0 View
Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for...
28 April 2020 1,904 3 View
Hi all, I am a newbie in the field of classical MD calculations for biomolecules, and I am running a few calculations for studying protein-ligand interactions using the GROMOS force field in...
28 April 2020 1,811 0 View
I would need to check the distance between the two centers of mass of a Protein and of an organic Ligand (the resname and the resnumber of the ligand are both known), inside a system containing...
23 April 2020 4,057 4 View
I have tried the electrochemical impedance spectroscopy (EIS) for a series of electrode materials in two different electrolyte solutions but surprisingly I came up with two completely different...
21 April 2020 6,720 0 View
I want to run an MD simulation using gromacs for metal ion bound protein. I need to know the parameters as well as the force-field used for this kind of simulation.
18 April 2020 3,630 1 View
Hello everybody, I'm trying to analyse secondary structure of a protein with do_dssp included in the program gromacs. My trajectories are of 200 ns each. when I run gmx do_dssp, it takes very long...
04 April 2020 484 3 View
I'm using gromacs to simulate a lipid bilayer by MD and I'm using tip3 as water model. How can I calculate the volume per water molecule ? Thank you in advance.
03 April 2020 3,893 1 View
Currently I use Gromacs to perform molecular dynamics of tobermorite 11A, but it turns out that this structure has a monoclinic box, I need to solvate my structure only above in the z axis, but I...
27 March 2020 1,523 3 View
I have performed simulation for Protein-Ligand complex in Gromacs. While in system preparation I have given: gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 2.0 -c and ran simulation for...
26 March 2020 6,937 5 View
Dear all, Hi. I would like to do simulation for my full protein model (including transmembrane domain) extracted from Cryo-EM reported pdb file. I have used Orientations of Proteins in Membranes...
26 March 2020 8,789 0 View
Hi everyone. I have a trajectory that was calculated by Gromacs. 1) How can I calculate an h-bond lifetime between two selected amino acids (for example Arg32 (from A chain) and Glu 21 (from B...
23 March 2020 9,848 3 View
I have installed the ubuntu and Gromacs. I also installed the VMD. It says VMd installation is complete. Enjoy! But I cannot open the VMD window! When I try to open vmd, I get all these notes but...
21 March 2020 10,115 4 View
Greeting to all, I have modelled two different domains of the same protein from two different tools (example - 1-250 using ab initio and 250-400 a.a using modeller). Now to make it a full length...
17 March 2020 2,969 5 View
1. I am processing my umbrella sampling simulations using the Weighted Histogram Analysis Method in Gromacs (gmx wham). However, I would like to report the mean dG and a standard deviation. To do...
16 March 2020 1,759 3 View
Hi, I am familiar with performing MD simulations using Gromacs on protein-ligand complexes. However, BAR is a new technique to me and I need specific clarification of the decoupling sequence...
13 March 2020 3,964 1 View