Force fields in GROMACS 4.5.5

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Number of calcium ions for my system

I have to simulate protein in 400mM calcium ion conc. I will neutralise the system with chloride ions. My system now has 265 protein residues and 18610 water (SPC) molecules. How many calcium do...

03 April 2013 5,980 2 View

Protein simulation in the presence of calcium (400nM)

I want to do an MD simulation in gromacs on a protein to study the effects of calcium conc (around 400 nM). I want a good protocol to introduce calcium ions in to the system to have the desired...

02 March 2013 5,802 10 View

How to find potential inhibitors for a protease.

i have a papain-like protease but having Chymotrypsin-like activity due to non-canonical active site Serine. I have to find inhibitors for this protease with in-silico methods. Can i dock...

31 December 2012 5,928 3 View

3 residues are outliers in a ramachandran plot

I have done homology modelling and then refined the model with MD in gromacs. Then I did clustering of trajectories and selected the average structure of the model. Finally I did energy...

31 December 2012 4,204 13 View

Protein modeled with I-TASSER server.

But 2 of its disulphide bonds out of 5 are missing and I have information on the disulphide bonds and want to include them in to model. I also want to do Molecular dynamics on protein with...

31 December 2012 6,044 2 View

Molecular dynamics of protein in gromacs in presence of calcium.

I want to study the structure changes of proteins in presence and absence of calcium ion. The calcium concentration would be 400mM and the phenomenon of interest is sec. structure changes, local...

31 December 2012 4,440 8 View

I have done a molecular dynamics simulation in gromacs on a protein and want to find phi and psi angles for a residue.

I want to get the psi and phi angles on a particular residue and plot them on ramachandran plot. I went through some tutorials and was informed to use ndx file for that. But can someone give me an...

31 December 2012 4,327 6 View

B-factor from PDB and RMS fluctuation graph from MD

I have MD simulated a homology model in gromacs. I have obtained an RMS fluctuation graph for the same. Can this graph be compared with a PDB file which has b-factors generated during X-ray...

31 December 2012 701 1 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 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

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View