How to use make_ndx in GROMACS version 4.5.7?

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What could be the "physical significance" for the electrochemical circuit used to model EIS data ?

Hello, I have a two compartment electrochemical cell. I have put a nanoporous aluminum oxide membrane (nominal pore diameter = 20 nm) between these two compartments. Now I looked at the impedance...

10 November 2017 8,029 4 View

Is there a thermoresponsive liquid that does not mix with water?

Hello,I am looking for a thermo-responsive liquid which will not mix with water. The idea is to have two small connected reservoirs , one containing this liquid and the other having water. Then,...

11 December 2016 9,326 3 View

Is there a software tool for creating biomolecular structure for MD simulations ?

Is there any software tool to create the following : (1) DNA nulceotides with one S-H (thiol) group at its tail (2) To form an Au-S bond between the thiol and a layer of gold atomsI would like to...

01 January 1970 9,914 7 View

How to measure the current flow across a membrane ?

Hello,I have an electrochemical cell consisiting of two chambers. These two chambers are separated by a membrane.Now, I want to observe the flow of current across this membrane for different...

01 January 1970 5,204 4 View

How to calculate the mean force from PMF values?

I have a Potential of Mean Force (PMF) values obtained against a reaction coordinate in a file. This was generated using a pulling molecular dynamics simulation. I am thinking of taking numerical...

01 January 1970 3,670 8 View

Can I use PRODRG for generating a GROMACS compatible topology file for a non standard nucleic acid?

My nucleic acid PDB file consists few non standard residues where the uracil, cytosine bases have been modified by adding methyl, phenol etc groups to them. Can I use PRODRG to generate a topology...

01 January 1970 1,949 3 View

How to create a ss DNA structure having a quadruplex in PDB format ?

Hello , I want to create a PDB file for a ss DNA molecule having a quadruplex in it. I have checked the web and also here and got to know about a few webservers / softwares which can be used to...

01 January 1970 4,523 4 View

How do I add a new DNA residue to the terminus of my DNA PDB ?

I want to add a new DNA residue to the existing terminus of my DNA PDB file. How can I go about this task?? Can I use PyMol or Chimera ?

01 January 1970 5,110 2 View

How do I create a Au-S bond on a layer of gold in PDB format for use in MD simulations ?

I have created DNA and protein residues in Chimera for use in MD simulations. I would like to know about different ways to create a layer of gold atoms and a Au-S bond in PDB format so that it can...

01 January 1970 6,302 2 View

I have a PDB file in which many protein residues are missing and this produces an error when I use pdb2gmx (GROMACS) , what can I do to fix it?

The protein is missing many residue parts and when I used pdb2gmx with the -maxwarn function I found that the total charge on the protein was + 5.269 electron units. How can I go about in fixing...

01 January 1970 4,544 11 View

Can formaldehyd-fixed gelatin be melt?

I am puzzled about the properties of gelatin, when used for tissue-embedding. Hard gelatin can be melt again by temperatures about 40°C. Formalin-fixed gelatin is like crosslinked protein and...

07 August 2024 1,686 1 View

How to fix errors in my heat transfer steel structure with reinforced concrete slab model Abaqus?

I have modelled a steel structure using beam elements in Abaqus and attached to this structure reinforced concrete slab. The analysis that I am making is heat transfer of the structure. The...

07 August 2024 1,028 0 View

How do I replace a file with a more recent version of a paper that was uploaded to ResearchGate?

The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...

07 August 2024 9,934 3 View

Can I use a HisTRAP column for affinity chromatography?

I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...

07 August 2024 505 3 View

How to solve g_mmpbsa error?

Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out

07 August 2024 6,066 0 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

How do you delete a duplicate pdf for the same paper on ResearchGate?

The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.

07 August 2024 9,508 1 View

Unusual intensity drop in some sections of chromatograms in DDA?

Hi, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...

07 August 2024 3,218 4 View

Microtome tissue sectioning - How to prevent chatter of paraffin tissue specimen sections?

Hello everyone, I have recently started using the microtome device for sectioning of paraffin-embedded mice lung. While I had some success in sectioning and observing proper ribbons, some of my...

06 August 2024 666 4 View

AUX gas reading problem on QE with full MS and PRM method in one run?

Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...

06 August 2024 4,953 0 View