12 Questions 61 Answers 0 Followers
Questions related from Xiaoquan (Chris) Sun
Dear all, My study is using Molecular Dynamics Simulation to investigate biological or chemical systems. My recent study is testing the stability of BSA at different conditions. I find...
10 October 2016 464 8 View
Dear all, I am investigating an ionization process, the change from CH3CH2COOH NH3 to CH3CH2COO- NH4 in the water. I used Gaussian with implicit water to optimize geometry to find which state has...
12 December 2015 4,278 4 View
I got a new assignment. The problem is to find a preferable interaction between two simple molecules. One is a cation and R-COOH, the other is the cation and R-COO-. I was asked to use Gaussian...
12 December 2015 5,320 2 View
I am a little confused about the workflow of MD simulation. The initial velocity of particles in a system is given according to Boltzmann distribution at different temperature. And then Verlet...
11 November 2015 8,171 6 View
I am preparing new MD simulation system contains Na2SO4. The research is about the salt-out effect for protein in salt solution. I prefer to use AMBER for the simulation. I find an ECC force field...
10 October 2015 9,121 3 View
My title is not the exact description for my problem. I was asked to calculate the free energy change of cation (Na+, K+) with acid group (COO-) on a protein using QM/MM method. I used MD...
09 September 2015 1,224 4 View
Hi, I am doing MD simulation of a polymer in TIP3P water now. The monomer has a 7membered ring. With AMBERTOOLS15, I used PARAMFIT to get a set of force field for it. I used TLEAP to combine...
08 August 2015 2,053 4 View
I was asked to do OPT in Gaussian with different temperatures. Previously, I did not take temperature into account. And I used the following command. #p MP2/6-31G* opt Afterwards, I added...
08 August 2015 9,029 10 View
I need to calculate the solvation free energy of a solute in dimethylacetamide (DMA). Since AMBER does not have the force field for it. I am testing whether I could use GAFF as DMA force field....
04 April 2015 1,196 5 View
I was asked to use MD simulation to measure the spring constant of a polymer chain. I didn't find any references about this. It seems that people use AFM to do this. I plan to run ordinary MD...
03 March 2015 3,040 3 View
Sorry about the confusing title. I am talking about the output frequency to write the trajectory file. Normally, the time-step in MD simulation is 1 or 2fs. And I am using 1ps/frame to output the...
01 January 2015 7,873 11 View
Dear all, I am running a MD simulation of polystyrene with AMBER. It looks the benzene ring on the backbone distribute evenly. My advisor asked me to find a way to evaluate the behavior of the...
12 December 2014 9,604 2 View
