How to add extra molecules in MD simulation?

Dear researcher, I want to simulate my protein with the denaturants (MW-139 Da). I am using Gromacs 2018.2 version and the extra molecules were added by using gmx insert-molecule command. I want...

01 February 2019 1,509 3 View

Regarding generation of DNA topology using Gromacs?

Dear researcher, I want to simulate a protein-DNA complex. I can simulate the whole DNA but i want to simulate the nicked DNA. When i try to generate the topology of...

10 November 2017 4,277 0 View

Too many LINCS warning?

Dear researcher, I want to simulate my protein in different concentrations of Guanidinium chloride. I successfully added 4M GdnHCl in a cubic box. But when i want to neutrilize the system with the...

10 November 2017 9,007 0 View

How to simulate selenium containing enzyme in Gromacs?

Dear researcher, I want to simulate a selenium containing enzyme. But when i processed the selenium containing enzyme using pdb2gmx command so it is showing an...

09 October 2017 6,044 11 View

About free energy landscape calculation using Gromacs?

05 June 2017 4,631 5 View

How to predicted the Stable structure from MDS?

02 March 2017 7,404 6 View

Please provide me urea.gro and urea.itp files for MDS?

01 February 2017 7,836 4 View

About mm-pbsa calculation?

11 December 2016 5,709 6 View

About diamer dissociation from MDS study?

10 November 2016 8,445 5 View

About Principle Component analysis or Essential dynamics?

Dear researcher I am facing a problem in principle component analysis. I calculated the eigenvalue by g_covar command. After that i saw in many Literaturrates they give the percent value. In...

09 October 2016 4,751 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

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 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

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 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