Please anyone to help in preparing qm/mm input files by "namd" (Molecular Dynamics software) for a ligand-enzyme complex?

Hi All, I'm trying to prepare qm/mm files for a ligand bound to an enzyme, I followed the tutorial of "vmd" and "namd", but it still reports an error in qm calculations. Any idea please? Best,

08 September 2018 808 0 View

Can anyone please help in finding the Fourier transform of the distance equation?

Can anyone please help in finding the Fourier transform of the distance equation? The distance equation is: (Z2-Z1)2+(Y2-Y1)2+(X2-X1)2=D2 X1,Y1,Z1 are the coordinates of the first point. X2,Y2,Z2...

04 May 2017 131 3 View

I need simple executable to perform steepest descent minimization for protein structure (pdb)?

Hi all, I need simple executable to perform steepest descent minimization for protein structure (pdb), with instruction how to do it? Thanks,

10 November 2016 7,700 1 View

How to Call NAMD Molecular dynamics software from *.bat file on windows?

09 October 2016 7,401 0 View

How I can apply random incremental pulse search (RIPS)?

Hi All, Can any one please tell me how I can apply "random incremental pulse search" (RIPS) for side chains of amino acids interacting with certain ligand. Which software (with link to the...

08 September 2016 1,726 0 View

Can anyone please explain if there is any software to produce coarse-grained 3D structure for RNA and DNA?

05 June 2016 3,303 5 View

Where can I find forcefields for phosphoserine to use with "NAMD"?

05 June 2015 7,007 6 View

In Molecular dynamics, which ensemble is better to use: NVE or NVT?

We use different ensembles in MD, which one is preferred to use?

02 March 2015 7,295 14 View

How can we solve the problem of energy drift in NVE ensemble in Molecular Dynamics?

How can we solve energy drift problem in NVE (constant energy, constant volume, and constant number of particles) ensemble in Molecular Dynamics?

02 March 2015 1,207 3 View

In Molecular dynamics (NVE), is energy drift of about +5 Kcal/mol.ns acceptable?

In Molecular dynamics (NVE ensemble), is energy drift of about +5 Kcal/mol.ns acceptable?

02 March 2015 3,680 2 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

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

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 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

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