CHARMM22/CMAP vs. CHARMM36?

I'm currently running a protein simulation on GROMACS. I was originally using CHARMM22/CMAP for the simulation, but with some reasons I decided to switch to CHARMM36. The thing is, I expected...

10 November 2020 8,906 1 View

Meta-analysis: How to calculate variance of log response ratio from SE of raw response ratio?

I am working on a meta-analysis using log response ratios. In one of the primary studies the results are presented as raw response ratios with associated standard errors. How can I calculate the...

04 October 2020 6,098 3 View

[HBV DNA] Getting smear instead of bands. Why?

I extracted HBV DNA from serum (frozen, stored at -80 degree). I used Qiagen's HotStarTaq Plus PCR Kit to amplify the region encompassing the preS1, preS2, S gene. the product is 1373bp long.The...

25 May 2020 8,715 1 View

What test is best to compare responses of sub groups with data gathered through Likert scales?

Dear fellow researchers, I'm a newbie when it comes to SPSS but have manged to analyse data gathered through Likert scales reliably enough so far when comparing different groups of respondents...

10 October 2018 436 5 View

How do I interpret the output of Procrustes and Cointertia analyses?

I compare two large data sets (13 observations of 300 and 4000 variables respectively) using Procrustes rotations and Coinertia analyses in R. I am able to generate the plots but struggle with the...

18 March 2018 1,279 1 View

What is the best solvent for extraction of 1,4-Butanediol diglycidyl ether (BDDE)?

18 October 2016 7,138 3 View

Has anyone got any experience with extracting DNA and RNA from single zebrafish larvae - after WISH?

26 August 2015 2,149 3 View

Recommendations for software/website to carry out self-paced reading experiment *online*?

I have only ever worked with Linger so far, which cannot be used over the internet. I heard about Paradigm, but it seems participants would have to have both Dropbox and Paradigm installed to take...

08 August 2015 3,069 14 View

H3K9me3 ChIP primers for positive control - can anyone help?

Hello all, We're currently implementing a ChIP protocol on mice liver to analyze the binding of some TFs and the distribution of various histone modifications. One of These is H3K9me3. Our current...

09 October 2014 2,608 7 View

I wonder if the question harms to others include children as well and in if so how?

We are here in Uppsala in Sweden studying harms to children when parents have drug or alchol addiction problems. That is why I am interresting in the results of your project. I also wonder when...

01 January 1970 9,437 4 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

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

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

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 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