Xiaoquan (Chris) Sun

5 Questions 35 Answers 0 Followers

Questions related from Xiaoquan (Chris) Sun

Big potential difference between conformation in MD simulation and optimized conformation in Gaussian?

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...

17 August 2015 4,944 3 View

Gaussian OPT in different temperatures?

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...

07 August 2015 8,956 9 View

Difference between Potential of Mean Force and Free Energy Profile?

I know this question is stupid. I do MD simulation with AMBER all the time. But I am still confused about some basic concepts. Recently, I got stuck of using SMD to calculate PMF. I had the value...

29 April 2015 7,309 7 View

Any suggestion on the method to use MD simulation to measure polymer spring constant?

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...

31 March 2015 2,280 3 View

How do I evaluate the behavior of ring structure of a polymer?

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...

10 December 2014 5,962 2 View