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Questions related from Vijayakumar Gosu
Hello all, I have generated a MD simulations data with triplicates and now i want to analyze the similarity between the replicates using first 10 eigen vectors. I have preformed PCA...
07 July 2018 6,494 0 View
I have performed simulations for Protein RNA complex around 1500 residues. I have used triclinic box with 1.4 nm distance from the edge of the box to protein as triclinic box takes less number...
10 October 2017 1,472 1 View
I have installed gromacs 5.1 in server which has 4 nodes each with 40 CPUs. I am allotted to use only 2 nodes with 80 CPUs. after installation when i did sample md run only 20 cpus are being...
09 September 2017 9,671 3 View
I am preforming MD simulations using gromacs for protein-RNA complex. According to the previous reports, it is clear that Histidine forms an interaction with the phosphate back bone of RNA and...
09 September 2017 389 1 View
I am currently working on drug complex, i am using OPLS-AA force field, i have to generate a topology file for ligand compatible to gromacs using OPLS-AA. any suggestions please... Thanks in advance
06 June 2015 5,807 2 View
Hello everyone, I have downloaded the POPC128.pdb from http://wcm.ucalgary.ca/tieleman/downloads. As 128 lipid molecules are not enough for my receptor (GPCR) I am supposed to increase the number...
04 April 2015 9,057 5 View
Hello everyone, I am currently working on membrane protein and i am trying to simulate my protein using gromacs 4.6.5. I am following the below link....
04 April 2015 5,252 3 View
I wanted to calculate binding free energy calculation of my complex (protein +inhibitor). I have no resources to calculate for large number of frames (ie, 5000 frames from 100ns) hence I have...
10 October 2014 3,628 10 View
While taking the average structure from GROMACS simulations of a complex, which average structure is reliable? For example in GROMACS there are three options ox (average), oq(bfactor) and...
06 June 2014 8,056 1 View
I have done 100ns simulations for my protein using gromacs, and then subjected to PCA analysis from gromacs (g_cova, g_anaeig). In order to see the dominant motion within the proteins (WT and...
06 June 2014 5,604 4 View
In order to construct unphosporylate kinase, I have replaced phopothreonine with threonine from active crystal structure computationally, as there is no inactive crystal coordinates for my kinase....
05 May 2014 5,972 0 View
I have run dynamic simulations for kinase protein with gromacs package using gromos force field for 100 ns. At the end of simulations, molecule is out of the box. So how to center the molecule...
11 November 2013 6,675 4 View
I subjected ATP bound kinase (ATP+protein+2MG2+ ions) for 100ns simulations using gromos force field in Gromacs package. When I analysed the trajectory, the nucleotide end of the ATP (Adenine+...
09 September 2013 5,012 0 View
I read in a paper entitled" http://www.tandfonline.com/doi/abs/10.1080/08927022.2011.561430#.UjAD1TZmWSo". However i couldn't understand from this paper as i am new to MD and Autodock
09 September 2013 386 2 View
