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Questions related to Molecular Dynamics
I'm a newcomer to the area so I would like a parameter file for sphingosine that I can use straightaway in VMD. If anyone is willing to share then I'd be very grateful.
15 March 2019 5,936 2 View
hello. i have finished running the ensemble docking with ligand library. what are the next step of computational methods or other methods available to prove the top scored molecules likely to be...
09 March 2019 3,284 7 View
I came across this question while studying Tuckerman book on Statistical Mechanics for Molecular Dynamics.
04 February 2019 2,149 3 View
Hi, I would like to study how a large protein complex interracts with a ligand. Due to the sheer size im afraid im limited to Coarse Grained. Im guite confident about the protein, however the...
29 January 2019 1,733 3 View
I am aware of the force field specific to bond formation that is compatible with LAMMPS however, the system I am simulating alone is computationally taxing already and adding LAMMPS to my...
10 January 2019 8,389 2 View
I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotate this molecule to have my acyl chain along z-axis. Then I created 8x8 down layer...
12 December 2018 6,112 2 View
I am interested in doing some in silico mutational analysis on a single loop of a 350-400 amino acids protein and test the mutants for docking (easier part). What would realistically speaking the...
12 December 2018 1,037 3 View
Hello everyone! I am interesting on host-guest inclusion complexes using quantum and molecular modeling technics. I ve done docking with vina software. Now i am intersting if i could do MM-PBSA...
01 December 2018 4,352 3 View
However whenever I try to minimize the geometry with forcite module, either it fails or disorder the adsorbent structure after the optimization. What is the problem? Is there an issue with the...
26 November 2018 6,493 4 View
I have an enzyme (human HMGCoA reductase) which has four active sites. The experiments had been carried out before from which IC50 values of several molecules were calculated. Now I'm about to...
25 November 2018 7,131 11 View
Hello! I trying to do some molecular dynamics with DNA structures, where I am checking how 5' phosphate affects the interaction. However, in common force field such as AMBER, no charge set was...
19 November 2018 3,886 4 View
Hi, What is the easiest way (software) for protein-SWCNT (single wall carbon nanotube) binding site prediction? Eventually, I want to know what is the sites on the protein(s) with the highest...
22 October 2018 7,118 2 View
I am constructing a protein based hydrogel, using collagen like peptides. I would like to know how many waters and proteins are needed to have the desired system concentration of 10% w/v in silico...
15 October 2018 406 3 View
Hi, I want to calculate the 1- angle between slab surface plane and water molecule plane 2- angle between OH vector of water and slab plane. How should i define OH vector, HOH plane and surface...
13 September 2018 2,191 0 View
I am a researcher who uses ReaxFF to simulate new materials and in the study of several large scale systems. The use of such a tool would be quite beneficial for my group.
12 September 2018 7,152 0 View
I filled out the relevant form here: http://cpmd.org/download/accept-license/cpmd-license-application I have waited more than two weeks and have concerns about my application.
11 September 2018 9,256 1 View
I have imported a MD trajectory in VMD. I need to generate plots like how the distance between two selected atoms is changing over the simulation. Is there a way to do this in VMD? Thanks.
22 August 2018 2,732 3 View
Recently I've tried to use the following...
21 August 2018 3,471 2 View
After simulations, how to write the pdb file of a particular frame in VMD (containing protein +ligand)?
21 August 2018 715 7 View
I am trying to calculate the defect formation energy of ABX3 type perovskite. I don't understand how to calculate the charged defect formation energy.Suppose, I am creating a vacancy A by removing...
20 August 2018 5,095 0 View
I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run? Thanks.
01 August 2018 4,078 3 View
I am using reaxff and also using reaxc pair potential . i am doing molecular dynamics by using lammps get some output files(log.lammps,species.out,bonds.reaxc). which tool used for analysing the...
30 July 2018 5,323 3 View
How can i model the deposition metal on metal by Sputtring Process using MD lammps ?
28 July 2018 7,735 3 View
I want to make Al/SiC structure in material studio. how can i do it? there is pure Al structure and SiC structure in material studio software. I want to delete group atoms from bulk of Al and...
24 July 2018 809 3 View