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Questions related to Molecular Dynamics Simulation
i am currently using xleap for snake venom toxin fasciculin, and was trying to add ions using the command addIons.. but i receive that error. the script says (addIons fasciculin C1- 4). any...
09 April 2021 4,307 1 View
If my protein is large and has many domains of which one domain has the active site that I want to study ligand interaction for with MD simulation, can I cut out the domain of interest in the...
03 April 2021 8,045 3 View
I have performed a 100ns simulation of a protein-ligand complex. Now I want to get the final structure of the complex after simulation and superimpose it with the initial structure. What is the...
01 April 2021 8,512 4 View
I have run peptide-DNA (single stranded) complex simulation. I understand that the helical structure of ssDNA can not be intact during simulation. But, I wonder how to determine the most feasible...
27 March 2021 973 2 View
I couldn't find the .cif file in COD or Material Project. Space group should be P-3m1 (buckled structure).
25 March 2021 8,018 2 View
I will use molecular dynamics simulation for the refinement of more than two protein structures. Most of the research for refinement in the literature is about the docking of two proteins. So I...
24 March 2021 6,107 3 View
I want to keep the position of my ligand(F420) fixed and should not move out of the initial position soo much.What can i do it restrain it from moving?? I have also attached the image which shows...
22 March 2021 8,374 5 View
Hi,everyone!I want to ask that:After the AC containing the polymer chain is optimized, water molecules are added, and then molecular dynamics simulation is performed. How to see how much pressure...
17 March 2021 3,457 2 View
The simulation is a Coarse-Grained simulation, and I went through the following steps: (1) Put position restraints (PR) on protein+lipid heads first (this is done in multiple steps, with position...
16 March 2021 2,324 7 View
In any MD simulation done using LAMMPS, what does negative total energy at every step mean? Further, what does 0 E_mol and negative E_pair depict? Can you please suggest a text or brief...
16 March 2021 451 6 View
I have tried gromacs for MD simulation I have separated the lig molecules from my protein and then added force field i.e charmm36, during the time of water model selection I have choosen the...
12 March 2021 7,169 4 View
According to the gromacs manual, setting 'gen_vel = yes' for production generates initial velocities for particles, and setting it to 'no' doesn't. I set it to 'no' and my simulations still work...
12 March 2021 5,098 9 View
I am interested in peptide self-assembly study by MD simulation. The peptide self-assembles into fibrils at low pH. I use Avogadro program build the peptide monomer in an extended conformation....
12 March 2021 622 1 View
Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...
02 March 2021 9,017 4 View
I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...
28 February 2021 5,022 1 View
I am working on a preparation of representative polymeric structures of some popular polymers, such as polyimide or PTFE for MD simulation, during which a single nitrogen or oxygen atom will be...
25 February 2021 8,333 3 View
During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...
24 February 2021 5,286 8 View
I need to carry out molecular dynamics simulation on Aluminium alloy. For this i need the crystal structure that which could be further replicated to form a structure.
23 February 2021 1,627 1 View
Everything tells you the derivative of Xi, but not how integrate the value to implement it into a simulation. How do you do this?
22 February 2021 6,618 1 View
I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...
21 February 2021 3,556 3 View
Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.
21 February 2021 1,966 1 View
I am learning MD simulations using GROMACS and while I was doing a protein in water MD simulation a doubt raised. I was following the steps mentioned on the tutorials page and it said The system...
16 February 2021 5,751 4 View
I am trying to do some MD simulations of a protein with zinc ions. I am trying to use a charmm forcefield (I have tried 2017 and 2021) and Gromacs. I get an error when doing pdb2gmx Residue 'ZN'...
13 February 2021 9,609 2 View
Hi, If I am performing an MD Simulation in which the two groups/molecules are moving in a direction on applying a force on the system, how would I calculate the velocities/acceleration of the two?...
09 February 2021 9,664 4 View