In plumed, is it possible to access the atoms index (for a given CV) in bias section?

How can we access the information on the atom indexes involved in a given collective variable. I can see that it is possible to access this information in colvar and analysis classes. But is it...

03 April 2019 7,112 2 View

No title

1. What should be non-bonded interaction parameter for the atoms of the wall? 2. How to ensure its correctness? Thanks

10 November 2016 6,314 0 View

Reduction in speed while using ReaxFF forcefield on LAMMPS. Is there any specific reason for this?

03 April 2016 2,106 6 View

How to put distance constraint between two groups of atoms in LAMMPS package?

I have two groups of atom of moving particles. So how can I put the distance constraint, without making them rigid.

02 March 2015 5,582 0 View

What are the two oxidation states of sulphur in sodium thiosulphate?

Please explain with proper reasons... Thanks.

01 February 2015 6,561 7 View

How to draw a cone along a given vector?

please explain .

01 February 2015 5,894 0 View

What are the two oxidation states of sulphur in sodium thiosulphate ?

In thiosulphate, two sulphurs have oxidation state of -2 and +6. (as per suggestions). Sulphur bonded to three oxygen is considered to have +6 (Sulphur A) and other sulphur has -2 (Sulphur B)....

01 February 2015 4,298 7 View

How can I make a conical selection in vmd?

What are the general equations for a conic selection. I want information about the atoms present in a conic volume of given radius and height. Please explain.

01 February 2015 1,690 3 View

Why neighbour list is not building on GPU in LAMMPS ?

01 February 2015 3,596 1 View

Why does ortho nitro aniline form only 2% on performing nitration of aniline?

Nitration of Aniline in Conc. H2SO4 and HNO3, we can understand the formation of both para and meta nitro aniline. But what is the reason for the poor yield of ortho nitro aniline?

10 November 2014 1,954 7 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

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

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View