14 Questions 9 Answers 0 Followers
Questions related from Akanksha Gupta
I know how to change the ionic concentration by -conc command but, what is the default ion concentration that gets set while adding ions for neutralization in gromacs?
03 March 2016 5,929 7 View
hello all, i have a system with 122046 water molecules and i want to add 2mM calcium ion concentration to the system. The current net charge on my system is -3. Now, i am trying to use the genion...
01 January 2016 9,607 1 View
which forcefield suits the best for divalent metal ions like calcium in protein in gromacs system and why. the calcium makes bidentate bonds with protein and water.
10 October 2015 253 1 View
Hello all, As far as I know, minimization is done before simulations but are there cases when the simulated structure still needs further refinement?
06 June 2015 3,832 6 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...
04 April 2015 4,875 4 View
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...
04 April 2015 9,760 8 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...
03 March 2015 6,377 6 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...
02 February 2015 2,704 1 View
i want to perform simulations in gromacs using gromos53a6 forcefield. when i apply positional restraints to ions. it gets invoked. but now i want to restrain bound water for which i have generated...
02 February 2015 7,309 5 View
I wish to do md simulations for a protein bound to calcium and water. I am able to generate the .itp file for calcium but how can I generate a .itp file for bound water in my protein?
01 January 2015 6,537 3 View
I would like to run molecular dynamics of a protein in which I have many calcium ions and disulfide bonds present . Now there are 2 problems: 1) Why when running GROMOS53a6 forcefield, it says...
01 January 2015 4,856 4 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...
01 January 2015 5,469 17 View
hello all, I used refcoord scaling=com in npt equilibration and now running production phase with positional restraints on calcium ions in my protein when i get this warning: "you are using...
01 January 2015 10,012 2 View
My protein comes out of the water box after gromacs simulations. what to do?
01 January 2015 2,371 2 View
