19 Questions 8 Answers 0 Followers
Questions related from Neha S Gandhi
I am interested in simulating RNA/DNA with phosphorothioate backbone. I am aware of the old parameters in AMBER force field. Could anyone point to recent publications or force fields to perform...
05 May 2019 2,865 2 View
Selenium nanoparticles (SeNPs) have shown vital prospects in cancer medicine and nutritional science. Has anybody tried to create SeNPs from their hexagonal lattice cell and model them using...
12 December 2018 7,285 4 View
I have gone through carbon nanotube guide on GROMACS website. http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube I have a nanotube aligned to z-direction. I am trying to simulate...
10 October 2017 4,167 2 View
I am running a system with protein and carbon nanotube using GROMACS 5.1.4. I used position restraints for carbon nanotube however, during NPT run (both protein and carbon nanotube fixed),it...
10 October 2017 1,457 3 View
There are many papers on MD simulations of proteins with carbon nanotubes using AMBER force field. I was wondering if anybody can provide parameters (frcmod or lib files) for carbon nanotubes in...
08 August 2017 522 1 View
I know the size of nanoparticle and number of lipids in system. A 5nm gold nanoparticle has ~4000 atoms. A paper suggest lipids:Au ratio = 0.98 % wt/wt. How can I calculate the number of gold...
07 July 2017 5,653 2 View
I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration...
03 March 2017 1,223 2 View
I have a pdb file of coarse grained lipid monolayer system consisting of 64 DPPC lipids. The pdb file is missing box information. I am interested in simulating nanoparticle penetration in...
02 February 2017 2,660 1 View
Is there any publication reporting simulation of chitosan using Glycam06 force field?
12 December 2016 2,100 0 View
I was wondering if anybody has worked with chemistry of these two cross-linkers and have characterised by FTIR or MS whether they are cis/trans or S/R isomers? Apologies: I am not a synthetic...
09 September 2016 8,627 4 View
I have come across papers where protein adsorption is studied using molecular dynamics simulations on HAP 001 face. I would like to know if OH of HAP is involved in interactions with protein...
08 August 2016 1,713 2 View
Dear list, I am trying to simulate protein unfolding on hydroxyapatite surface using AMBER MD package. I got the parameters for HAP (based on the interface force field). I prepared the system...
08 August 2016 6,870 0 View
The weak CH-pi hydrogen bond has currently been highlighted in biomolecules. I am interested in monitoring/calculating CH-pi interactions (if present between sidechains of aromatic residue and...
07 July 2016 9,421 3 View
I have performed PCA analyses using gmx covar and anaeig tools in GROMACS. I want to calculate the percentage and cumulative percentage of the motion explained for the eigenvectors and obtain a...
07 July 2016 3,313 4 View
I want to perform MD simulation using molecular mechanics force fields. The system consist of SWNT covalently linked with CH3 or COOH groups on the surface. How can I build and setup system for...
07 July 2016 7,303 5 View
I have performed REMD simulation of a 25 residue long peptide. In advanced sampling techniques such REMD it is not recommended to plot parameters against time e.g. secondary structure along time...
10 October 2015 4,536 3 View
I have a polymer with a single amino acid sidechain and some linear linker groups. CD studies indicate presence of peptide like beta structures. The structure is very compact in solution as seen...
03 March 2015 6,136 7 View
I am aware of the tutorial and guidelines for REMD by Mark Abraham on GROMACS website. I have 48 replicas, I calculated temperatures using the REMD temperature calculator server where the exchange...
03 March 2015 6,316 2 View
I have previously used normal modes calculation in MMPBSA/GBSA methods in AMBER. I am aware of the tool called CENCALC, which is more simpler approach for conformational entropy calculation....
09 September 2014 1,248 5 View
