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Questions related to Molecular Dynamics
I have been working with a complex system that involves 5 different atoms and 3 different molecules. However 2 of the atoms are present in 2 different molecules i.e O & H. Now when I am...
11 March 2020 4,660 2 View
Hi everyone, I have a pdb file which is a trajectory of one protein. How can I use VMD to classify the frame of the protein according to the conformation and draw several images which image...
05 March 2020 3,923 4 View
I started a new project and I want to simulate co2 adsorption By a molecular simulation Method. Please recommend some books regards
25 February 2020 1,208 4 View
In theory, dH/dL (or dV/dL in thermodynamic integration) originated from the difference in enthalpies of two distinct states lambda and lambda+dL. I wonder how the Gromacs module calculates the...
25 February 2020 2,056 3 View
Hi everyone! I'm starting to learn how to perform Replica Exchange Molecular Dynamics (REMD). At this point, I'm interested in perform those simulations in GPUs, but the resources I have are...
30 January 2020 4,302 2 View
I am trying to do a simulation on Materials Studio that was performed on LAMMPS (doig2014). It is about an adsorption of surfactant molecules onto solid surfaces, and the aim is to calculate the...
23 January 2020 1,616 1 View
Dear all, I'm simulating the CO2 adsorption on two graphite sheets using the LAMMPS software and I calculated the density profiles in the pore width. Now I would like to compare the results with...
21 January 2020 4,270 1 View
I want to simulate a lipid in coarse grained Martini scheme, i used vmd tutorial in this link: http://www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf after using its topology file...
21 January 2020 8,317 1 View
We simulated (LAMMPS program) the tensional behavior of CNTs with different chiral indexes (10, 10; 0, 10, and 10,0) using the original CH.airebo potentials (Stuart et al., 2000). The plot...
17 January 2020 8,274 3 View
Am trying to calculate melting point of Silicon based on free energy methods in LAMMPS, I want some literature/theory for calculation of reference system free energy i.e. Einstein crystal for...
17 January 2020 937 3 View
I am using LAMMPS software and in doubt wether the approach to increase pressure is right or not. As increasing pressure in few nanoseconds is practically possible or not.
14 January 2020 8,586 1 View
I am performing protein ligand simulations in Gromacs. In md simulations how can one fix these dangling movements of residues near protein terminals? I think this will interfere in my RMSD or...
14 January 2020 4,119 3 View
Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command: trjconv -f md_0_10.xtc -s...
13 January 2020 7,394 5 View
Head-space Shimadzu GC-17A gas chromatography (Shimadzu Europa GmbH, Duisburg, Germany) was performed by using a flame ionization detector for the quantitative determination of sevoflurane loading...
03 January 2020 1,096 1 View
Several alkali-activated aluminosilicate materials (e.g. Metakaolin, fly ash)are shown to be a polymerized structure. The three stages for the production are dissolution of raw materials...
03 January 2020 1,473 2 View
Dear all, I made a bilayer consisting of Al/Al2Cu (Metal/Intermetallic structure) using lammps, when I start simulation it gives this error: ERROR on proc 0: Neighbor list overflow, boost...
18 December 2019 9,455 1 View
i want to perform molecular dynamics (MD) simulations on fe3o4.i looked thorough literature but did not find something useful.can anyone help me with its potential and partial charges?
08 December 2019 6,679 2 View
I've optimized the initial structure setting forc_conv_thr=1.0D-6 and etot_conv_thr=1.0D-5, however, when I want to start MD with the optimized structure, QE failed with error at the first md...
06 December 2019 4,004 3 View
I created a MGDG membrane I want to know how can I calculate number of water molecules which create hydrogen bond with lipids per lipid. Gromacs can only calculate number of all hbonds between two...
05 December 2019 9,118 2 View
Hi all, I have a rather naive Molecular dynamics question, though functionally useful. I am simulating a rather large structure on a congested HPC, and was wondering if there is an accepted...
01 December 2019 10,013 2 View
Hello, Can anyone inform me on the techniques (other than semi grand canonical or grand canonical ensembles) that one can use to calculate the equilibrium impurity (say P) concentration in...
22 November 2019 5,249 3 View
I am working on some more complex membrane simulations and wanted to know if there is a specific advantage to using a certain ensemble. It seems as though most people have used either NVE, NVT, or...
21 November 2019 1,359 3 View
I have a membrane-protein system prepared using CHARMM-GUI. Now, I want to place some ions near the protein towards the extracellular side, intracellular side and inside the protein as three...
11 November 2019 3,642 10 View
Dear experts, I am trying to match the spontaneous polarization value of BaTiO3 using PBE functional from the following paper -...
11 November 2019 8,722 9 View