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Questions related from Nandan Kumar
Dear all, This is regarding the Steered Molecular Dynamics. After finishing SMD, extracted useful frames from the SMD trajectory and performed the brief NPT equilibration of the selected useful...
12 December 2019 6,846 2 View
Hi Everyone, I am calculating the surface area per lipid of 200 ns membrane trajectory using MEMPLUGIN of VMD and it seems to be calculating the same too slow. Therefore, I would like to ask Is...
06 June 2019 3,452 4 View
I would like to calculate the energetics for open shell singlet Sc+ and Sc+(OH2) using CCSD(T) level. As if we consider default Gaussian procedure, it seems to be considered close shell singlet....
12 December 2018 8,977 0 View
Dear all, I would like to ask to you all that I am performing the ONIOM calculation and want to calculate radial distribution function. So, Please let me, can I calculate radial distribution...
07 July 2017 1,308 0 View
I am running the MD simulations for 30 ns which is 15000000 nsteps using dt= 0.02 using GROMACS software but it has terminated (after 13000000 steps) before completion due to queue limits. I would...
06 June 2017 7,451 10 View
As we know that density analysis is one of the worthwhile analysis to validate the our bilayer membrane model. I am using the gmx density of gromacs software to calculate the lipids headgroup...
06 June 2017 2,030 1 View
Basically, I want to calculate the torsion angle potential (Vn) for the force field parameter development. For that I performed the potential energy surface (PES) scan with rotating a bond by 360...
12 December 2016 6,567 13 View
I need to construct a mixed lipid bilayer for simulating a membrane protein. I am trying in GROMACS, but I have a problem in orientation of protein in lipid mixed type lipid bilayer.
06 June 2015 3,696 4 View