i want to know that this loss of atoms does not cause errors in simulation results?
What particular forcefield are you using? Have you noticed any other hydrogen atoms missing? Might it be part of a united atom forcefield model?
I plot thickness.dat files with xmatrix and gnuplot but I cannot plot area per lipid.dat files neither with Xmatrix nor with Gnuplot. Does anyone know the corresponding command line for Gnuplot...
06 July 2016 299 2 View
I simulated DPPC60%-DMPC40% +1AFO model membrane with Gromacs 4.5.4 and now I'm in analyzing step. I wanted to calculate area per lipid headgroup and bilayer thickness of the membrane so I used...
05 June 2016 6,930 0 View
I want to make movie from my molecular dynamics simulation outputs. Pymol was suggested to me, when i read its tutorial, i noticad that it is more usefull for mac systems. can any one guide me...
31 December 2015 8,816 1 View
I'm trying to use GridMAT to get the area per lipid and thickness so I installed activeperl on my laptop (on windows) and put the three necessary files in and ran this command:> perl...
11 December 2015 2,052 2 View
In the simulation of KALP15 in DPPC, when we run grompp command, one of the outputs is mdout.mdp. can we use these files for our energy minimization step, after making necessary changes?
08 September 2015 2,972 0 View
I used to remove all water crystals from pdb file before starting simulation same az what I learned from "lysozyme in water" justine tutorial, but I met some one in a seminar, who told me we must...
06 July 2015 1,635 6 View
I simulated DPPC60%-DMPC40%+protein bilayer system for 100 ns. Now I want to run another simulation for 50 ns on this system. I wonder if its nessecery to use .cpt file from the previous md run. I...
01 January 1970 2,667 0 View
Dear users I ran simulations with 128 DPPC/DMPC .I have the output of 10 ns simulation. If I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which...
01 January 1970 2,141 2 View
I tried four trials of the same Copper Phosphides sample in Alkaline medium ( 0.5M KOH) with Hg/HgO reference electrode and Pt as counter electrode. I used 0.001 V/s scan rate for first three...
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If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...
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I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
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Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...
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Global ‘Weather’ has stopped, as ‘aqua thermionic instituted by the ‘Global thermo atmospherics has instituted global thermodynamics of 120º C + and thus all waters are, or have boiled into a...
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Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
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kindly reply me. Thanking you in advance.
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Hello. I am working on ROS production of two systems: system A is cerium oxide and hydrogen peroxide, system B is cerium oxide nanoparticle, hydrogen peroxide and potassium bromide. I did some...
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