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Questions related from Xiaoquan (Chris) Sun
Dear All, I am good at MD simulations with AMBER, NAMD, Gromacs, Forcite... But not familiar with MC simulation. Could you suggest some MC simulation packages? I have to calculate the binding...
27 July 2017 2,096 12 View
Hi, I am working on 1MVM at http://www.rcsb.org/pdb/explore/explore.do?structureId=1MVM. I find this crystal structure is constructed by 60 identical fragments based on its crystal structure. The...
04 May 2017 7,481 2 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...
17 August 2015 5,010 3 View
It's been well-known that the potential of staggered ethane is 2.9kcal/mol lower than that of eclipsed ethane. It should be straightforward to calculate this with Gaussian. The eclipsed ethane is...
11 August 2015 5,785 5 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...
07 August 2015 9,034 9 View
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 7,365 7 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...
31 March 2015 2,338 3 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...
10 December 2014 6,020 2 View
