gmx_mmpbsa, error,
You can try Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
GROMACS that cames with gmxMMPBSA is not working.
Use an external version of it (or recompile it inside the conda environment)
Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?
01 March 2021 3,422 3 View
Incompletely cross-linked pdms are difficult to remove.
01 March 2021 798 3 View
I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??
28 February 2021 2,153 1 View
Dear All, I am doing my MS in Electronic Businesses. And I am interested in the AI field and its applications for businesses, its benefits, impacts, etc. What kind of scientific research dominate...
26 February 2021 8,816 6 View
Most of the papers have compared different hyperparameters such as layers, initializers, activation function, and optimizer algorithm in the CNN algorithm for detecting network intrusion. This is...
24 February 2021 4,578 4 View
At first please see the attachment. This experiment was performed for a period of 7 days (n=100). After 7 days, we found different level of survival rate (%) for each treatment. Now, I want to...
15 February 2021 9,145 2 View
The organo montmorillonite nanoclays modified with octadecylamine were used for the experiment. After acid treatment, the surface area will be increase. However, in my experiment, the surface area...
10 February 2021 1,581 3 View
Dear all, I am trying to optimize a bimetallic complex using # opt=tight b3lyp/lanl2dz scf=qc geom=connectivity. The program is running for around 5 days but the size of the .chk remains same...
05 February 2021 8,721 3 View
Do anyone have a full MATLAB code for structural topology optimization using Genetic Algorithm? Such as a cantilever beam? Could you provide some MATLAB code to me , a beginner for GA. Thank...
03 February 2021 3,789 5 View
The recommended amount of DNA for restriction digestion is 1ug in a 50ul rx I've got around 500-600ng of DNA in a total volume of 35ul. Would I get satisfactory results with this amount of DNA for...
31 January 2021 729 6 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
I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...
02 March 2021 1,830 3 View
Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...
02 March 2021 7,161 3 View
I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...
01 March 2021 3,610 1 View
01 March 2021 1,290 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
I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...
28 February 2021 4,966 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
Hi, all! How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials? I have not find the choice for explicit element in Abaqus CAE. I am wondering whether it is possible...
25 February 2021 9,936 2 View