Sk Jahiruddin

10 Questions 44 Answers 0 Followers

Questions related from Sk Jahiruddin

How do you simulate an unnatural base pair inside DNA?

I want to perform a molecular dynamics simulation for an unnatural base pair inside DNA. I have done the parameterization of individual base pairs, terminating the pair-sugar junction by methyl...

10 October 2014 8,450 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...

10 October 2014 3,109 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.

09 September 2014 1,828 10 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...

09 September 2014 4,658 2 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...

09 September 2014 6,722 12 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.

09 September 2014 3,463 7 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...

09 September 2014 8,151 4 View

How can I calculate the basis set superposition error in gaussian?

I'm optimizing DNA base pairs in gaussian. I have optimized base pairs individually and in pair both. Right now I want to find the basis set superposition error in those optimization.

08 August 2014 6,369 2 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...

08 August 2014 9,947 3 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...

08 August 2014 5,756 1 View