How do you simulate an unnatural base pair inside DNA?

09 October 2014 8,330 7 View

What is the main difference between equilibration and production run in NAMD?

I am not understanding the parameters need to change in equilibration and production run conformation files. NAMD tutorials file always use "reinitvels" to equilibrate and that also in a same...

09 October 2014 2,937 9 View

What is Born Openheimer Molecular Dynamics (BOMD) and how to use it?

I need to know about the use and utility of BOMD. I have gone through the BOMD keyword in gaussian but it was not clear enough. Please tell me how can I use BOMD in gaussian or any other software.

08 September 2014 1,733 10 View

How to optimize a structure in the presence of electric or magnetic field in gauusian 09?

I want to optimize a structure in the presence of electric or magnetic field field in gaussian 09. I didn't find the keyword "Field" in gaussian 09 mannual clear enough for me. Experts please explain.

08 September 2014 3,371 7 View

How useful the CHARMM parameters generated by SWISSPARAM?

I want to perform a basic level of molecular dynamics with some unknown residue to check the stability of the molecule in 300K with aqueous environment. My study would be simple with no complex...

08 September 2014 6,608 12 View

Can stability of a molecule be predicted from BOMD/ADMP in gaussian?

I have run 1 ps (pico-second) simulation for formaldehyde using ADMP as implemented in gaussian 09. I got periodic association and dissociation of bonds and structure. The potential energy were...

08 September 2014 4,548 2 View

Why am I getting error while using IOp(3/107 and 3/108) with wb97 functional in gaussian?

I'm trying to use IOp(3/107=0400100000,3/108=0400100000) with wb97 functional in gaussian 09, but I get error termination every time. nThT2=3 NYI in PrismS.Error termination via Lnk1e in...

08 September 2014 7,978 4 View

What is the meaning of "fullSamples" keyword in ABF calculation in NAMD?

While doing Adaptive Biasing Force calculations in NAMD we need to provide the keyword "fullSamples" the default value of which is 200. What is the significance of this keyword? How do I provide...

07 August 2014 5,675 1 View

Why do we divide the region of interest in different windows in ABF in NAMD?

While performing Adaptive Bias Force method free energy calculation in NAMD we divide our region of PMF (Potential of Mean Force) in different windows and then merge the .pmf files performing...

07 August 2014 9,875 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

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 2 View

High aspect ratio hexahedral mesh optimization solver?

I am interested in evaluating mesh optimization solvers that converge to high aspect ratio unstructured hexahedral grids. In other words, I am interested in a solver that optimizes warpage,...

26 February 2021 7,279 2 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

How to interpolate from a time-series database ?

Hi, I am having trouble with a problem, in the field of Optimal Control and the generation of optimal time-series. Let's consider a system, whose dynamics are represented by dx/dt =...

24 February 2021 9,105 2 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

What might be the reason for obtaining two bands in plant genomic DNA extraction?

I got a thin band and a thick band i guess it would be the genomic DNA and the 260/280 ratio is 3.

21 February 2021 6,523 6 View