Dear All,
I would like to ask if anyone knows of any server that can give the gromacs 53A6 ff topology. I have to prepare my protein in that topology and use it. The ATB server is now only fixed at 54A7ff.
Any ideas?
I am using annual time series data to estimate a VAR model in R. However, when I run the command to find the optimal lag length, I get the following error: Fehler in VARselect(data, lag.max = 10,...
18 February 2021 9,647 3 View
because many technical steps are there to get a particular plant nano particle and its expensive too
14 January 2021 1,556 4 View
for example the total volume is 50microliters how can we know that what will be the amount of template , buffer, enzyme, primers (forward and reverse), dNTPs, MgCl2 and water?
02 January 2021 3,352 6 View
Final concentration for each component in master mix depends on what or how it will be known that in this master mix the concentration required is __ microliters ?
02 January 2021 5,764 2 View
Im refering to Andy Field's example in his book Discovering statistics using SPSS, 3rd edition, page 728, where he gives an example of a data structure with level 1 variable is a memory recall...
26 December 2020 9,717 6 View
For image processing, I am using ImageJ. I need to separate the features from the background and calculate pixel intensity of features and background. Can anybody help me in this? Thanks
09 December 2020 7,472 9 View
If we have three different domain of data (e.g. security, AI and sport) and we did 3 different case study or experiments (1 for each domain) and we estimate the Precision, Recall and F-measure for...
07 December 2020 9,833 3 View
Is there any conversion formula for this purpose.
06 December 2020 3,283 3 View
How can stem cells repair damaged cells? Could anyone provide papers show the therapeutic potential of stem cells in vitro (on the disease model)?
29 November 2020 9,534 6 View
As we know, computational complexity of an algorithm is the amount of resources (time and memory) required to run it. If I have algorithm that represents mathematical equations , how can estimate...
25 November 2020 6,950 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
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
Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...
24 February 2021 8,856 3 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