Farideh Badalkhani

5 Questions 3 Answers 0 Followers

Questions related from Farideh Badalkhani

How can I determine the protonation state of a phosphorene sheet in acidic and neutral pH conditions?

Dear experts, I am going to perform an MD simulation on a system including water and phosphorene sheet in different pH conditions (low and neutral pH). However, I do not know if the different pHs...

31 December 2018 9,680 1 View

WARNING: Listed nonbonded interaction between particles X and Y at distance ... can anyone please help me with this problem?

Dear all, I am trying to perform free energy calculations of a small drug in octanol using the GROMACS 5.1.3 software. I built a box of octanol using the following command gmx insert-molecules -ci...

12 March 2018 871 0 View

What is the most stable conformation of Chalcone at acidic pH?

Dear Experts, I need to know what is the most stable conformation of Chalcone at low pH environment. The attachment is Chalcone's structure. Regards, Farideh

09 March 2017 4,056 6 View

What is the reason of blowing up a system in a simulation?

Dear all, I am performing a MD simulation on a branched polymer through GROMOS 53A6 force field. But, I don't know why when I execute the energy minimization, the system blows up. I have attached...

05 September 2015 7,905 3 View

How can I find the active site of a protein with docking?

Could you tell me if there is any way to finds the active site of a protein with docking?

18 January 2015 1,767 6 View