Error in gromacs MPI installation.?

Hi everyone, I am installing gromacs(2019) on my desktop. I could successfully install gromacs but when building mpi version it shows the following error. I have applied all the possible ways,...

04 May 2019 6,254 5 View

30-50% of MS Spectrum detected from tissue samples are unmatched with the available protein database?

30-50% of MS spectrums are detected from Tissue or Cell samples are unmatched with the available protein sequence database? Can anyone suggest a methodological flow for this problem. Thanks!

09 October 2018 7,105 3 View

Features extraction from protein 3D structures?

Hi Everyone, I want to extract features from proteins 3D structures. Can anyone suggest a methodology, software or server to carry out this process? Thanks in Advance.

09 October 2018 5,354 0 View

How can we merge different Microarray datasets from GEO for DEGs Analysis?

Hi Everyone, I'm using microarray data to identify DEGs and map its PPI network but now I want to use multiple datasets reported by different studies in Acute Myeloide Leukemia (AML). Please...

02 March 2017 7,564 7 View

I'm trying to do a comple simulation in Gromacs but it is showing the following Error, how to solve this?

Residue 97 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the input file. Perhaps your atom and/or...

01 February 2017 4,138 1 View

I am having continous problem in ./runn.in file when using Amber 12.?

After completing MD the following error is showing again and again. Anyone please. Error: Could not set up parm file prmtop for reading.Error: Could not open parm prmtop CPPTRAJ: Trajectory...

10 November 2016 7,347 9 View

I am having a problem while using Amber for MD simulation?

05 June 2016 5,593 6 View

Journal of Medicinal Chemistry publishing fee?

31 December 2015 8,719 3 View

Homology modeling of a proteins sequence length 3390 amino acids?

I want to build Homology model of a protein whose sequence length is 3390 amino acids. Please let me know is it possible to build the homology model of such a large protein and if so how far we...

31 December 2015 7,632 7 View

Does RMSD vary with protein sequence length?

RMSD is usually taken as below 2 but if the length of Proteins is too high or large, is it affect RMSD or not? if, then how much it vary from sequence to sequence

11 December 2015 7,798 3 View

How to analyze a particular region of my simulation box in GROMACS?

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

How do I increase the yield of my PCR product?

Hello, We would like to increase the yield of our PCR product. We are running a series of PCR reactions that is targeting ~1.1kb sequence. We begin each reaction with ~400pg of template DNA...

02 March 2021 4,029 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

1 nm thick MgO thin-film to be deposited on Si wafer using thermal evaporation. What will be the optimum deposition conditions?

Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.

28 February 2021 3,640 3 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

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

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

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

How does GROMACS calculate the average structure of proteins?

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

How to identify or create correct list from GROMACS options during analysis of trajectory ?

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

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 View