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Errors in GROMACS

md simulation gromacs protein-ligand simulation written 5 weeks ago by nilanjanamani88 • 0 • updated 5 weeks ago by cpad0112 ♦ 14k

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Trying to find out permeation events in each pore of AQP protein embedded in lipid bilayer through VMD

vmd md simulation tcl-scripting permeation-events written 11 weeks ago by iqrakhan9192 • 0

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182

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SLURM: running equilibration steps for MD simulation

md simulation slurm sbatch written 6 months ago by asma.nounna • 0

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892

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"Atomtype O not found" error in gromacs 5.1.1

md simulation gromacs written 17 months ago by SS • 0

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1.4k

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GROMACS fatal error

md simulation gromacs written 2.3 years ago by amitunited0532 • 40

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Need to know the importance of prediction

md simulation structure prediction written 2.5 years ago by sakshisingh.bioinfo • 30 • updated 2.5 years ago by WouterDeCoster ♦ 44k

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1.1k

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MD simulation using YASARA

md simulation written 3.5 years ago by sakshisingh.bioinfo • 30

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1.2k

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how much time should i run MD simulation to check stability of predicted structure?

md simulation written 4.0 years ago by rajeshkumar_vinod • 30

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892

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Lipid Nanoparticle Interaction- MD Simulation

lipid nanoparticle interaction md simulation written 4.1 years ago by Zaved Hazarika • 0

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1.0k

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Unexpected Molecular Dynamics results

md simulation written 5.0 years ago by f.dehghanian68 • 30

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Recent Replies

A: No color observed in Colour Key of HeatMap.2 by morty • 0
Hi, It is likely because of this line: col1 <- colorRampPalette(c("green", "black", "red"))(4...
A: Variant Call Format (.vcf) conversion to .bam by swbarnes2 ♦ 8.5k
To quote another poster in these parts, what you are asking is like asking how to turn a steak in...
C: Differential Abundance Analysis wih DESeq2 and metabolites as continuous predict by greenm11 • 0
Hi, Sorry I should have made it more clear: I repeat this process for each timepoint that has i...
C: testing set for RNA-seq AML by Ali • 0
Thanks for your reply I use TCGA data was fine to download and run the analysis where the sampl...
C: empty fastq files created by docker bcl2fastq2 v2.20 OSX by akh22 • 40
The input folder appears to be intact, containing everything original except the samplesheet.csv...
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I had to google for m3vcf: https://genome.sph.umich.edu/wiki/M3VCF_Files > is there an automa...
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it seems that characteristics of overlapping SNPs is that there is not many of them who have very...
C: testing set for RNA-seq AML by newbio17 • 230
Have you tried [GEO][1] or [cBioPortal][2] to see if they have any dataset you could use? [1]...
C: RNASeq data: STAR low alignment score by newbio17 • 230
If you want another method of checking for rRNA to double check, you can try `split_bam.py` from ...
C: Transcriptome analysis of two closely related plant species by Istvan Albert ♦♦ 84k
yes, you can split a bam file by chromosome, and spawn a separate process with gnu parallel
C: Compare transcriptome between different species of Leishmania by Dunois • 20
`Prokka` with eukaryotes though? Leishmania spp. are eukaryotes.
C: Error running cutadapt in multithread mode by Francesco • 10
Thank you, I created a conda enviroment for cutadapt with python 3.7 and now it's working in mult...

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