please guide me
hi. i run adfr for docking purpose but give permission denied error and i dont know how can i resolve it please guide me.
04 May 2018 1,228 1 View
i play simulation and for review of fluctuation and must view xpm file and use from xview for this file but this program unsupported image type.how i can this type file?
31 December 2017 5,347 0 View
hi i play simulation by gromacs. i run nvt and npt and my system equilibrate. how can i understand my simulation how much time need?
31 December 2017 5,711 3 View
hi i play MD simulation but, between temperature of nvt and npt is different.is this normal? if no whats factor of this? and why in this pictures rmsd in nvt is different to rmsd in npt state?
31 December 2017 975 5 View
salaam dostan man danshjoye olompezeshki tehran hastam mikham bebinam kodom ostad dakhel kodom daneshgah dar tehran gromacs ra dars mide khastam beram sare klasesh?
31 December 2017 7,279 0 View
for secondary structure analysis by gromacs 5.07 i need to install dssp but i dont know how i can install .please guide me
31 December 2017 5,876 4 View
hi i need to some vector which contain signal peptides for example ompA or pELB IN SNAP GENE.
09 October 2017 1,637 0 View
05 June 2017 1,771 1 View
this antibody trend attach to IgE
05 June 2017 2,393 0 View
hi dear friends. i run a simulation on my server. my server has 8 CPU core and 640 GPU core, but during of simulation don't used from 100 percent power of CPU core. how can i resolve it?
01 January 1970 2,540 2 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
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
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 have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.
18 February 2021 4,822 2 View
I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...
17 February 2021 1,066 3 View
I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...
15 February 2021 5,561 3 View