I want to simulated a RNA, which has Co (2+). How to get the parameters for Cobalt & where to add them ?
I am working on nucleic acid (NA). I have to add K(+) ions to study its behaviour. I want to keep the coordinates of NA molecule and K(+) fixed & allow water molecules to equilibrate. This...
03 April 2017 989 2 View
I have got the following error after executing the grommp command before energy minimization. Fatal error:number of coordinates in coordinate file (ribo_solvated_ions.gro, 572158) does not match...
31 December 2016 1,858 8 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
Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue
02 March 2021 5,433 5 View
Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...
01 March 2021 9,332 6 View
I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...
28 February 2021 4,949 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 researchers, Hello Castalia3.2 researchers I am a beginner with Castalia, I work on optimization of RFID systems used in wireless body networks. I simulated a WBAN with 10 nodes and one...
28 February 2021 400 1 View
I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...
27 February 2021 356 6 View
Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...
27 February 2021 9,233 3 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