How to analyze root mean square inner product (RMSIP)?

Hello all, I have generated a MD simulations data with triplicates and now i want to analyze the similarity between the replicates using first 10 eigen vectors. I have preformed PCA...

06 July 2018 6,386 0 View

How good to use triclinic box for gormacs simulations?

I have performed simulations for Protein RNA complex around 1500 residues. I have used triclinic box with 1.4 nm distance from the edge of the box to protein as triclinic box takes less number...

09 October 2017 1,429 1 View

How to consider protonation states of histidine in Gromacs simulation?

08 September 2017 223 1 View

How can I utilize all the CPUs in one node during gromacs simulations?

I have installed gromacs 5.1 in server which has 4 nodes each with 40 CPUs. I am allotted to use only 2 nodes with 80 CPUs. after installation when i did sample md run only 20 cpus are being...

08 September 2017 9,639 3 View

Any suggestions on generating ligand toplogy using OPLS all atomic force field compatabile to gromacs?

I am currently working on drug complex, i am using OPLS-AA force field, i have to generate a topology file for ligand compatible to gromacs using OPLS-AA. any suggestions please... Thanks in advance

05 June 2015 5,768 2 View

How do you replicate the number of lipids in bilayer for membrane dynamics using gromacs?

03 April 2015 8,994 5 View

Using 20 frames (each 5ns ) from 100ns are reliable to calculate binding free energy calculations?

I wanted to calculate binding free energy calculation of my complex (protein +inhibitor). I have no resources to calculate for large number of frames (ie, 5000 frames from 100ns) hence I have...

09 October 2014 3,536 10 View

PCA and NMA approaches on MD simulation trajectory is same?

I have done 100ns simulations for my protein using gromacs, and then subjected to PCA analysis from gromacs (g_cova, g_anaeig). In order to see the dominant motion within the proteins (WT and...

05 June 2014 5,544 4 View

How reliable is the average structure of trajectory from gromacs simulation

While taking the average structure from GROMACS simulations of a complex, which average structure is reliable? For example in GROMACS there are three options ox (average), oq(bfactor) and...

05 June 2014 7,990 1 View

What are your suggestions on my unphosphorylation approach?

In order to construct unphosporylate kinase, I have replaced phopothreonine with threonine from active crystal structure computationally, as there is no inactive crystal coordinates for my kinase....

04 May 2014 5,924 0 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