embedded-atom method (EAM) potential and "upper limit" "lower limit"?

31 December 2016 9,811 1 View

How can I change of protein's primary structure by molecular dynamic simulation?

I work on the interaction of CNT and proteins. The results show that the tertiary and secondary structure of proteins are changed (effected by CNT). VMD sequence viewer shows that the primary...

07 August 2014 5,772 2 View

Why am I experiencing protein unfolding, and why are the number of H bonds increasing?

I work with gromacs code on the protein carbon nanotubes interaction. I saw that when the protein becomes unfolded, the number of hydrogen bonds (in protein itself, not with water molecules)...

07 August 2014 5,522 2 View

What is the number of h bond per molecule in EG?

I need to know the number of h bond per molecule for ethylene glycol.

05 June 2014 3,512 1 View

Deviation from Raoult's law in methanol water mixture?

I see that in some papers the reported methanol-water in 300K shows a positive deviation from Raoult's law, but at low temperatures have negative deviation from Raoult's law. Does anyone have a...

10 November 2013 8,755 4 View

Critical points for methanol OPLS-AA?

I need critical points as temperature,density and pressure of methanol with opls-aa force field.

10 November 2013 7,816 2 View

Is it possible to determine boiling point by lindemann index?

Is it possible to determine boiling point by lindemann index? I see some references, that work on melting point by lindemann index. But I need to determine boiling point by lindemann index.

10 November 2013 6,930 4 View

Hydrogen bonding and water methanol mixture?

I want to know that in methanol/water mixture from water rich to methanol rich, how change total hydrogen bonding in mixture? Less than pure water or not?

10 November 2013 3,904 6 View

Is it possible prediction Raoult's law by MD?

Molecular simulation and Raoult's law.

10 November 2013 1,478 5 View

Heat capacity and DL_POLY?

I need to calculate heat capacity from r.m.s fluctuation energy that reported in OUTPUT. How to do it?

10 November 2013 9,538 5 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

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 View