What is the default ion concentration in gromacs?

02 March 2016 5,898 7 View

Why is the -pq of calcium showing +1in gromacs while adding 2mM calcium ion concentration in the system?

hello all, i have a system with 122046 water molecules and i want to add 2mM calcium ion concentration to the system. The current net charge on my system is -3. Now, i am trying to use the genion...

31 December 2015 9,583 1 View

Which forcefield suits the best for divalent metal ions like calcium in protein system?

which forcefield suits the best for divalent metal ions like calcium in protein in gromacs system and why. the calcium makes bidentate bonds with protein and water.

09 October 2015 233 1 View

Is minimization required after MD simulations also?

05 June 2015 3,814 6 View

Can anyone help me with analysis of my NPT simulation in gromacs?

03 April 2015 4,852 4 View

How can I generate distance restraints between metal ions and its coordinating protein chain residues in gromacs?

can anyone please help me in guiding how to generate distance restraints between metal ions and its coordinating protein chain residues in gromacs. If i make index groups of my metal ions and use...

03 April 2015 9,739 8 View

Can Na+ ions used to neutralize the system diffuse into the protein in gromacs simulation?

02 March 2015 6,354 6 View

How can I solve the problem in restraining bound water in protein in gromacs?

i want to perform simulations in gromacs using gromos53a6 forcefield. when i apply positional restraints to ions. it gets invoked. but now i want to restrain bound water for which i have generated...

01 February 2015 7,288 5 View

Is anyone familiar with the use of the Force constant in mdp file?

I'm interested in doing a bunch of runs with slightly different restraint forces, I have certain queries regarding this: 1) how can I set a force constant and change it according to my need by...

01 February 2015 2,675 1 View

Can anyone help me with Refcoord scaling in gromacs?

hello all, I used refcoord scaling=com in npt equilibration and now running production phase with positional restraints on calcium ions in my protein when i get this warning: "you are using...

31 December 2014 9,884 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

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

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

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