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Questions related to Molecular Dynamics Simulation
I have run my MD simulation and i want to calculate the energy between my 2 chains, but i don’t know how to execute the ndx file? Thank you
30 November 2022 3,320 1 View
Input command : gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index_ligand_au.ndx -t npt.cpt -o pull.tpr -maxwarn 3 :-) GROMACS - gmx grompp,...
30 November 2022 7,666 1 View
I have run my MD simulation and I want to calculate the energy between my 2 chains, but i don’t know how to execute the ndx file? Thank you
30 November 2022 402 0 View
For example, I have quercetine as a ligand and cutinase as protein. If i want to carried out md simulations with different concentration of quercetine, how to do that? I want to do md simulations...
28 November 2022 3,356 4 View
Dear All, I am trying to simulate a ionic liquid-platinum surface system on gromacs. However, during the energy minimization, it shows to many LINCS warning during the execution and the execution...
28 November 2022 7,676 1 View
I have done a 50 nano second protein simulation using Gromacs and obtained an RMSD value greater than 3 nm. is it ok to proceed with it or is the value incorrect?
27 November 2022 4,826 2 View
What is the difference between a ligand's pKi value and its pKd value?
23 November 2022 5,748 5 View
Please suggest some reliable tools for computing multiple sequence alignment and generating heatmaps?
23 November 2022 6,540 3 View
Hello ,guys! I'm trying to balance my system with NVT, but the following error appears: Fatal error: Group Water_and_ions referenced in the .mdp file was not found in the index file. Group names...
18 November 2022 6,474 1 View
I have been looking for a way to create pdb files with a ligand in different protonation states. I came across this Dimorphite-DL: An open-source program for enumerating the io... article and...
14 November 2022 6,909 0 View
Where do I determine the various coefficients required to conduct simulations under the reaxff engine of lammps. I have a data file written with atom_style full, but I do not have any values for...
05 November 2022 4,713 1 View
During molecular dynamics, I'm facing the error mentioned above. How can we fix it, I checked the lig.prm file to see if it is missing some angle parameters but it doesn't seem so, the file is...
03 November 2022 2,389 1 View
I am using Gromacs MD simulation for protein-ligand complex using the following command after NVT Equilibration : gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx...
03 November 2022 6,748 2 View
Dear All, Could you tell me how to run MD simulation by any software. I have DS, VMD in hand. But I try to run 30 nsec in DS that spent 6 days, is that right? The reviewer asked me to perform...
31 October 2022 2,084 5 View
Hello everyone I am trying to use the MD simulation using cp.x code in quantum espresso. I am coping with a large fluctuation of ionic temperature when i run the NVT simulation. Could you give me...
28 October 2022 2,062 2 View
Hello all, I'm trying to understand how we can combine the Forward Flux sampling method with LAMMPS to obtain ice nucleation rates using mW potential of water? I do not understand if this is...
24 October 2022 9,184 2 View
I am working with an energetic material. using a classical forcefield how can I calculate isothermal compressibility by volume fluctuation formula, and coefficient of thermal expansion by the...
20 October 2022 7,224 4 View
I want to secreen plastic degarading bacteria and most of the methods has used PEG. But i don't know how to make the media with 2% PEG 6000.
18 October 2022 1,675 0 View
I am using scan to generate the PEC, but at the end point of scan, the resultant energy is different when I do single point calculation at the last point (25 Angstrom in this file). I don't know...
18 October 2022 757 2 View
Hi, I have recently experimented with GaMD in Amber18. When using only total potential energy boosting, the EGAMD_BOOST reached approx. 6. However, when I switched to dual boosting, the...
16 October 2022 4,434 0 View
Hi all, These days, I tried to move an insert originally in the TA cloning vector (pGEM-T Easy, Promega) to my target plasmid vector. I used SacII and NotI to cut TA cloning vector, ran gel and...
15 October 2022 288 3 View
Could anyone please help me to find out the best reference books for theoretical approach to crystallography and modeling?
11 October 2022 5,790 2 View
Greetings, I am working on MD simulations, specifically on CPPs and cell-membrane interaction. Can anyone please guide me on how I can extract the CA-atoms and P-atoms (Phosphorus atoms of the...
03 October 2022 9,078 0 View
Hello everyone, I am getting this error while running a non-collinear calculation in VASP. My MAGMOM tag does not exceed 255 characters. I have a total of 16 atoms (4+8+4) in my POSCAR file. Here...
29 September 2022 8,433 1 View