VMD's contact map plugin allows me to save the data in postscript format, but is there anyway I can write out the data straight from VMD's Tk console or something so that I can plot the data with other programs.
Hi all, I am working on a MD simulation of a membrane protein inside the POPC bilayer using namd. At first, I ran a short constrained dynamics by applying harmonic constraints to both...
05 June 2019 7,435 4 View
Hi everyone, My system is a dimer. During the MD simulation, I can see a strong hydrogen bond formed between two lysine residues which are at the side chains of two peptides. But, the issue is...
04 May 2019 6,105 5 View
Hi everyone, While using the PDB reader of charmm-gui for my membrane protein system which is a dimer, I got stuck at PDB manipulation option. It gives me option regarding...
04 May 2019 2,487 3 View
Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks
01 February 2018 4,939 3 View
Is there any standard value like two non-bonded residues or atoms are considered to form a contact if their distance is less than ? I usually use like 1.4 nm for short range non-bonded LJ cut-off...
01 February 2018 9,846 4 View
Are there any scripts or tools available in python to plot the running average of the data similar to as shown in the figure attached? Thanks
31 December 2017 2,525 4 View
I want to rotate a specific residue (say "resid 7 and resname MET") by 180 degrees around x-axis and save the coordinates. Can it be done using VMD's TK Console ?
31 December 2017 7,579 7 View
The characteristic frequency of thermal motion is around 7E12 Hz at room temperature (300K), but from that information how can we conclude that the bonds are hard; they don't vibrate !!
31 December 2017 6,084 2 View
I want to measure the tilt of helix with the normal of bilayer. My system is basically a dimer with two helices. Since using sidechain atom relative to the axis is optional, I simply defined...
31 December 2017 730 3 View
Are there any gromacs or other tools available to look for or find the number of protein-lipid contacts during Molecular Dynamics simulation of membrane protein ?
11 December 2017 2,812 3 View
Hi everyone, If you have written or come across any papers where Generalised Linear Mixed Models are used to examine intervention (e.g., in mental health) efficacy, could you please share the...
04 August 2024 4,130 4 View
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 View
HOW CAN I WRITE A CODE TO USE THE WAVENET TRANSFORM AS A FEATURE EXTRACTION METHOD INSTEAD OF DWT IN MATLAB?
03 August 2024 7,829 0 View
I want to write a topic for my PhD thesis in hospitality (hotels), can u please suggest some variables
29 July 2024 9,058 3 View
a 15-page paper
29 July 2024 1,956 5 View
In hirshfeld surface calculation i did not find any red spot in hirshfeld surface, is it ok for research article to write?
28 July 2024 2,988 0 View
Looking for paper collaboration writers: Collaboration Model 1: 1.1 Based on the chosen topic, complete the paper writing, select an SCI or SSCI Q1 journal, submit using my QRCID, and complete...
27 July 2024 8,965 1 View
Today, many priorities for improvements to teaching and learning are unmet. Educators seek technology-enhanced approaches addressing these priorities that would be safe, effective, and scalable....
26 July 2024 8,544 4 View
I am writing my thesis on the enculturation of Jamaican grief and bereavement practices that enhances their Christian faith and not diminish it.
23 July 2024 3,837 0 View
I am currently writing a systematic review
15 July 2024 9,176 1 View