How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

22 January 2015 5,376 2 View

How can I determine the Hbond occupancy with GROMACS?

Dear Gromacs users, I would like to run H-bond analysis in order to get a percentage H-bond occupancy between protein and DNA. How can I do it? I used the g_bond command but the obtained plot does...

29 October 2014 5,219 13 View

With regards to Gromacs Radius of gyration, how do I analyse the data?

Does anyone know how to analyse the plot obtained from gyration? I know what it means but I'm not sure how to use this measure or interpret data? I run MD for a protein in complex with DNA.

21 October 2014 9,021 1 View

Is it possible to run RMSD calculations in GROMACS?

Is it possible to run RMSD calculations for the part of the protein for example rmsd for AA 45-187? How to specify it using g_rms command?

15 October 2014 901 5 View

How do you calculate a hydrogen bond analysis between a residue and DNA in GROMACS?

How should I specify it after running make_ndx? for example r259 and DA2(from DNA). Does anyone know?

09 October 2014 3,390 3 View

Is there any (quick) tool to find a pentapeptide motif QL[SD]LF in common protein databases?

Representatives of this motifs are present in most sequenced members of the eubacterial, UmuC families and the MutS1. I found a paper from 2001 and would like to update the information (they used...

06 August 2014 1,789 1 View

How does one extend the protein simulation in Gromacs and check the total time of the MD?

I run MD simulations in GROMACS for 20ns which is 1000000 nsteps using dt= 0.02. I would like to extend it to another 20ns in order to have a complete run for 40ns. How should I proceed? According...

09 July 2014 9,457 25 View

Warning: pressure scaling more than 1% -GROMACS. Can anyone help?

I am working with gromacs and I have got a warning as shown below. Can you please suggest what to do to run my file completely. Please reply as soon as possible. I am awaiting your...

22 June 2014 9,824 9 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

How climate change will influences human and animal behavioral change?

The role of climate change influencing the human behavior as well as economics interest

01 June 2021 0 0 View

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 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

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 2021 0 0 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Guidelines for survey (question type) analysis?

Hi. Please tell me what guidelines should i need to follow for questionaries' type research work in India. It is not hospital based work, we are conduction basic institutional based qualitative...

03 March 2021 2,037 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