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Questions related from Akanksha Gupta
can anyone please help me in guiding how to generate distance restraints between metal ions and its coordinating protein chain residues in gromacs. If i make index groups of my metal ions and use...
23 April 2015 4,312 8 View
i have a gromacs system and after npt equilibration, the average preesure obtained by g_energy is 1 bar with a very low error state and low total drift. But the rmsd value given by the same...
17 April 2015 5,009 3 View
my system comprises of calcium depleted protein in spc water and i added sodium ions to neutralize the protein (as calcium were depleted so many sodium ions were needed) but after simulating in...
04 March 2015 3,186 5 View
I'm interested in doing a bunch of runs with slightly different restraint forces, I have certain queries regarding this: 1) how can I set a force constant and change it according to my need by...
18 February 2015 2,000 1 View
my production run generated 2000 frames but when i i load my md.gro and md.trr file in vmd, vmd shows only 252 frames. what might be the problem? why all the frames cannot be seen? also, i want...
29 January 2015 7,267 16 View
