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Questions related from Dilip H N
Hello, I have run a simulation of amino-acid +water system in GROMACS software. Now i need to get the water orientation profile (ie., how the water molecules are oriented w.r.t specific...
12 December 2017 4,457 4 View
Hello, I have ran a energy minimization, followed by nvt, followed by md run. My md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 30000000 ; [0.002 * 30000000 = 60000 ps (60 ns)]nstxout = 5000 ;...
05 May 2017 2,571 2 View
Hello,I want to calculate RDF of glycine of Hn-OW, Hn-HW, Ha-OW, Ha-HW, Ca-OW, etc.,So my commands were as follows... 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx > del 2 Removed...
03 March 2017 4,918 1 View
1] I want to solvate a protein with ammonia , how can i do it? Is there ammonia .gro/ammonia.pdb file available.? 2] How can i solvate with a mixture of solvents > eg., ammonia and water...??
12 December 2016 9,786 1 View
