Alexey Nikitin

12 Questions 79 Answers 0 Followers

Questions related from Alexey Nikitin

Are there automatic force field generators/services comparable in quality to OPLS?

What do you think about SwissParam, MolMeccano, GAAMP?

04 September 2017 1,623 4 View

What is the accuracy of the models of proteins embedded into membrane?

Is there a model that can be regarded as the standard for comparison? Are the coordinates?

30 December 2014 6,047 2 View

Can you recommend a good overview of halogen bonding?

Thanks.

09 December 2014 6,125 8 View

Why Urey-Bradley term largely abandoned in modern force fields?

16 November 2014 7,497 9 View

What quantum-chemical method is preferable to determine the dispersion interaction between the low-polar molecules?

24 September 2014 4,887 17 View

Why in today's force fields do we not consider explicitly 1-3 van-der-Waals interactions?

Such interactions are explicitly considered in the force fields of the 70s.

02 September 2014 832 6 View

Can the embedded atom method be applied for systems involving significantly ionic bonds?

Molecular Mechanics.

08 March 2014 467 1 View

What force fields are used for modeling strongly polar compounds?

I'm interested in polar compounds in which there is a significant contribution of covalence, for example alkaline earth metal halides.

03 March 2014 4,643 13 View

Is the hydrogen bond directed?

In some force fields, the hydrogen bond is described not only by the electrostatic term, but the angle one. Does this have any justification other than the crystallographic statistics?

14 November 2013 643 3 View

Why is AMBER12 based on AMBER99, but not on AMBER03?

Are there some problems associated with AMBER03?

16 October 2013 4,544 2 View

How to determine the orbital hybridization?

Are there any _formal_ rules which can determine the hybridization of an atom? For example, for PtH2 I can write different versions of platinum hybridization: sd1, sd5. How to determine the right...

12 September 2013 9,936 3 View

Which graphical MD program is the most convenient to build models?

06 August 2013 2,404 21 View