Does anyone know if there is a tutorial for Computational Alanine Scanning using GROMACS?
I am trying to run equilibration i gromacs 5.0.7 Implicit solvent. My input file is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps =...
11 December 2017 6,620 0 View
I am looking for a software for preparing nice (publication) pictures of sequence alignment.
02 March 2016 9,185 8 View
Does anyone know how to build a ssDNA in hairpin conformation? Does anyone know maybe other software where I could do this? Thank you in advance for any suggestions.
01 February 2015 8,333 6 View
Is there any fast way to change the DC on CYT for NAMD?
22 January 2015 5,376 2 View
I want to run dsDNA-protein MD simulations. I have tried to use top_all36_na.rtf Iprepared a script to run psfgen: package require psfgenresetpsf topology charmm36.nbfix/top_all36_na.rtftopology...
31 December 2014 171 9 View
31 December 2014 1,169 2 View
Dear Gromacs users, I would like to run H-bond analysis in order to get a percentage H-bond occupancy between protein and DNA. How can I do it? I used the g_bond command but the obtained plot does...
29 October 2014 5,219 13 View
Does anyone know how to analyse the plot obtained from gyration? I know what it means but I'm not sure how to use this measure or interpret data? I run MD for a protein in complex with DNA.
21 October 2014 9,021 1 View
Is it possible to run RMSD calculations for the part of the protein for example rmsd for AA 45-187? How to specify it using g_rms command?
15 October 2014 901 5 View
09 October 2014 3,037 7 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
Hello everyone, I had run a mediation model in SmartPLS using questionnaires that were already validated among my statistical population. A professor who edited my paper -though she is not...
01 March 2021 3,052 3 View
Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...
28 February 2021 5,650 1 View
Hello, I have three hypothesis to test, all with the same IV. I am testing if the effect of the IV on the first DV is mediated by awe. I am then measuring whether the effect of the IV on a...
26 February 2021 8,399 5 View
Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...
26 February 2021 10,014 3 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
25 February 2021 6,314 1 View
During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...
23 February 2021 5,065 8 View
Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.
20 February 2021 1,750 1 View
I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...
20 February 2021 3,309 3 View
I obtained a XRD diffractogram with significant broad band at low 2theta levels, also around 30 2theta another smaller broad band appears. It all points out to the existence of an amorphous phase....
19 February 2021 8,414 4 View