Are there molecular mechanical Force Fields for nitro compounds?

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

07 August 2018 9,310 3 View

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

What do you think about SwissParam, MolMeccano, GAAMP?

08 September 2017 4,968 5 View

On what software start experiments on protein folding?

07 August 2015 6,942 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.

05 June 2015 3,668 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?

11 December 2014 374 2 View

Can you recommend a good overview of halogen bonding?

11 December 2014 9,454 8 View

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

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

10 November 2014 3,926 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.

08 September 2014 9,184 7 View

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

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

08 September 2014 8,596 18 View

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

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07 August 2014 1,446 3 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View