How to use polarizable force fileds like Drude in NAMD ?

As stated in NAMD tutorial it is presently beyond the capability of the Psfgen tool to generate the PSF file needed to perform a simulation using the Drude model. So how can we generate suitable...

05 June 2019 6,456 1 View

In NAMD, should the flexible cell option turned on during NPT simulation ?

04 May 2019 8,687 5 View

How can I calculate the torsion angles of a specific residue side chain over MD trajectory in VMD?

I performed a 100 ns MD of a protein in an organic solvent and I want to calculate the change in torsion angles of a specific residue side chain over the simulation. is there any script to do that ?

06 July 2018 1,572 1 View

Namd OR Gromacs?

I have been using NAMD for one year now and I haven't used GROMACS yet. For those who used both of them, which one is more efficient?

04 May 2018 9,148 2 View

How can an organic solvent improve an enzyme activity ?

It has been known that most of the organic solvents have a detrimental effects on enzymes activity and structure but, if incubation of an enzyme in a specific organic solvent lead to an increase...

02 March 2018 5,703 6 View

What is the best concentration to study the effect of an organic solvent on enzyme?

I am studying the effect of different organic solvents on lipase stability. To compare the wild-type enzyme with it's mutants in terms of stability, should I work at very drastic conditions like...

02 March 2018 2,325 5 View

How can I run a repetition of MD simulation using NAMD ?

I performed a 50 ns production simulation for a protein in an organic solvents using NAMD. Now I want tp run a repetition for the simulation. I read about different approaches but I confused. can...

01 February 2018 1,881 7 View

SEM analysis of an immobilized enzyme on Eupergit C 250 L

05 June 2017 3,383 1 View

Using Bradford assay at very low protein concentration ?

03 April 2016 3,723 6 View

How do large proteins fold?

10 November 2014 1,235 4 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

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 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

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