Is there any publication reporting simulation of chitosan using Glycam06 force field?
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...
04 May 2019 2,906 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...
11 December 2018 7,309 4 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...
09 October 2017 1,493 3 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...
09 October 2017 4,206 2 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...
07 August 2017 557 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...
06 July 2017 5,680 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...
02 March 2017 1,249 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...
01 February 2017 2,732 1 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...
08 September 2016 8,660 4 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...
07 August 2016 6,889 0 View
We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...
08 August 2024 4,842 0 View
I am Looking for a Science Journal with good impact factor and low publication cost to publish a review paper. Your suggestions would be appreciated.
06 August 2024 6,796 3 View
Hello all, I wanted to know, can I use galaxy (USA, Europe or Australia) platform for analyzing the shotgun data, and can it be used for publication purpose as well? Thanks :)
06 August 2024 6,610 4 View
I attempted to make a privately uploaded text public but a window appeared that said an error occurred. There was no explanation provided as to why there was an error or what might be done to...
05 August 2024 8,025 7 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Nothing
01 August 2024 755 1 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
Survey on Productivity in Journal Manuscript Publication Survey Form Link: (https://forms.gle/YRVrn8dL4WZJJ79S8 ) Dear Researcher, We kindly invite you to participate in our survey focused on...
29 July 2024 4,116 1 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View