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 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

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.

07 August 2014 6,279 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...

07 August 2014 9,875 3 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How to find the right number of integration points in second order 3d finite elements?

I am familiar with finite element simulations and numerical schemes like the Gauss Legendre quadrature. I also know that the Gauss integration yields exact values for polynomials up to degree 2n-1...

27 February 2021 6,818 3 View

Is there an open source free software for text mining and sentiment analysis?

I am looking for a free software for text mining and sentiment analysis for my research on customer review mining (it involves calculating polarity of attributes,opinion oriented information...

25 February 2021 1,920 6 View