Molecular Dynamics

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Questions related to Molecular Dynamics

How to choose collective variables for ligand binding to protein?

Hello! What is the recommended way to choose collective variables / reaction coordinates to study ligand binding to a protein (e.g., for PMF free energy profiling)? I often see the advice like "Do...

11 March 2020 2,192 4 View

Is there any way to output LAMMPS readable data file which can identify similar atoms but in different molecules??

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 4,857 2 View

What methods are used to determine the localization and expression of a novel receptor?

09 March 2020 972 2 View

How can I use VMD to classify the protein according to the conformation and draw the analogous protein on one image?

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 4,034 4 View

What are the best molecular dynamics (and Monte Carlo) books in chemical engineering?

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 1,329 4 View

How is dhdl calculated in free energy calculation module of Gromacs?

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 2,236 3 View

REMD: Is it posible to run multiple replicas in a single GPU?

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 4,504 2 View

What the error on Geometry Optimization in Materials Studio means?

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 1,755 1 View

How can I make a comparison between LAMMPS results and lab results?

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 4,453 1 View

Can anyone give me a residue base coarse-grained(Martini) lipid toplogy file as sample for VMD ?

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 8,477 1 View

Why does Autodock Vina does not dock within grid box?

I'm working on a project whereby I want to prove I actually know what I'm doing with ADV, but something is not working out for me. For some reason every time I do a run using my ligand and...

21 January 2020 7,722 4 View

Are there any changes in the tensional behavior of single-wall carbon nanotubes (CNT) with different chiral indexes?

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 8,486 3 View

How to calculate melting point from Molecular Dynamics free energy calculations?

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 1,116 3 View

In molecular dynamics increasing pressure from, example 1 bar to 100 bar in few nanoseconds is right approach?

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 8,754 1 View

Dangling bonds in protein terminals?

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 4,261 3 View

GROMACS - why cannot load the xtc file (without PBC) to VMD?

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 7,611 5 View

Why we have a discrepancy in the results while measuring sevoflurane loading and simulating its binding affinity to SBE-βCD at different temperatures?

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 1,335 1 View

How to construct an therotical polymerized model for Na-aluminosilicate in MD simulation?

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 1,612 2 View

Can anyone explain the significance of appearance of 5 and 4 diffraction rings in SAED of AgNPs in terms of crystal nature?

SAED pattern of AgNPs reveals 5 (111, 200, 220, 311, 222) and 4 (111, 200, 220, 311) diffraction rings in two sets of reaction.

24 December 2019 7,223 5 View

Neighbor list overflow! (a LAMMPS error)?

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 9,625 1 View

Segmentation Fault during Minimization in AMBER ?

We are facing an segmentation error with two different class of proteins at minimization step in amber. A DNA-gyrase B protein and an ecto-nucleotidase. Both the PDB's are with optimal...

10 December 2019 3,545 2 View

Can anyone help me with fe3o4 potential and partial charges?

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 6,903 2 View

How can I solve the checkallsym problem when using QuantumEspresso?

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 4,277 3 View

How to calculate in GROMACS number of water molecules which create hbonds per lipid and water bridges?

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 9,282 2 View

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