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Questions related from Sk Jahiruddin
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 8,448 7 View
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 3,106 9 View
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 1,825 10 View
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 4,656 2 View
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 6,720 12 View
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 3,461 7 View
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 8,146 4 View
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 6,367 2 View
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 9,945 3 View
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 5,755 1 View