Alexey Nikitin

21 Questions 189 Answers 0 Followers

Questions related from Alexey Nikitin

Are there molecular mechanical Force Fields for nitro compounds?

I'm interested in the possibility of reproducing thermodynamic properties within 5%.

08 August 2018 9,411 3 View

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

What do you think about SwissParam, MolMeccano, GAAMP?

09 September 2017 5,085 5 View

On what software start experiments on protein folding?

What is better for a beginner?

08 August 2015 7,031 3 View

Do the molecular-mechanical models with bond restraints an improvement of any properties except for the specific heat?

Sometimes people justify the imposition of restrictions on the length of the bonds the fact that in such way simulates a quantum mechanical effect of "freezing" of high-frequency oscillations.

06 June 2015 3,759 2 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?

12 December 2014 471 2 View

Can you recommend a good overview of halogen bonding?

Thanks.

12 December 2014 9,562 8 View

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

11 November 2014 4,025 9 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.

09 September 2014 9,268 7 View

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

09 September 2014 8,697 18 View

What force fields are used for the calculation of protein interaction with metal surfaces?

08 August 2014 1,538 3 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 8,323 14 View

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

Molecular Mechanics.

03 March 2014 7,414 2 View

How to make the procedure of molecules overlay comfortable ?

I would like to write a convenient overlay procedure. What features should it have to be really comfortable for everyone?

03 March 2014 1,353 1 View

Are there simple universal molecular mechanic schemes for the transition elements?

I deal with VALBOND. Is there anything comparable in quality?

01 January 2014 5,262 1 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?

11 November 2013 628 3 View

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

Are there some problems associated with AMBER03?

10 October 2013 2,111 3 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...

09 September 2013 5,363 4 View

Is there an automatic tool for the classification of tertiary protein structure?

I would like to take the PDB file and get a description of its tertiary structure.

09 September 2013 7,470 2 View

Is it possible correctly describe the cyclobutane non-planarity in AMBER like force fields?

08 August 2013 7,628 4 View

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

08 August 2013 252 22 View

What is charge transfer?

In what solutions can we talk about it and why? Iodine in benzene, hydrogen bond in water, salt in water.

01 January 1970 5,119 3 View