I am trying to do a dft calculation in gromacs but don't know the code. Can anyone provide me the detailed code of the same.
I have just started to read about phenomenology and hence quite a beginner. I have observed hospital interactions between doctors and patients, noted down the conversations, added the non-verbal...
14 January 2021 3,452 3 View
I am trying to radio label PLA-PEG nanoparticles and wondered if I can purify the mixture via spin zeba desalting columns. I know the desalting column works for proteins, but not sure if it would...
29 October 2020 9,053 4 View
I have calculated spatial overlap of a species pair for two different seasons by using Pianka's niche overlap index. Here, I have used the frequency of occurrence of two species from camera trap...
23 September 2020 5,672 3 View
The tectonic models define paleocontinental assembly, the supercontinent Pangea has been disassociated into independent Laurasia and Gondwana, separated by a vast oceanic Tethys. Is there any way...
10 March 2020 7,824 3 View
Hi, I am new in SIESTA and using version 4.1-b4 for the transiesta calculation. But the following the tutorial videos, manual and examples the calculations are not getting completed properly...
15 January 2020 7,074 3 View
I have started a survey cum field study on the use of plants by local people of a particular locality. I have also documented the Phytodiversity of that location. Please suggest some statistical...
10 January 2020 8,626 12 View
I have a script which involves running certain pre-processing operations on the input file, which is generated by the meshing software Trelis. Before I can submit the job where I can easily define...
12 November 2019 6,055 1 View
We are aiming to isolate bacteria using membrane filtration. I would like to test for the probability of bacterial colonies growing towards the center of 47mm diameter membrane vs growing at the...
28 March 2019 9,790 2 View
Does anyone have the aquifer shape files for India please? Any help will be greatly appreciated Thanks
06 March 2019 6,117 2 View
In GIXRD measurement the incident angle onto the film surface is very low, so it corresponds to a large footprint of the incident beam as well. So, what should be the ideal dimension of the film...
22 January 2019 8,021 1 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, I spin-cast two different polymers onto wafers and measure their height as a function of initial concentration. For polymer A, I have the weight-average molecular weight (Mw) as well as...
28 February 2021 7,882 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
When I run the job for TS(QST3) in gaseous phase, it was completed without any error. But when I add water in CPCM model it terminated with an error: Inconsistency: ModMin= 2 Eigenvalue=...
21 February 2021 3,198 2 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
Hi all, I have a question regarding calculations using the Pfaffl method. I have 3 groups per experiment: 1 control group (calibrator) and 2 treatment groups with 6 to 7 biological repeats per...
19 February 2021 8,351 2 View