Most of the papers I have read on MD simulation of DNA is based on CG simulation. I am wondering if all atom atomistic simulation of DNA is viable or not and what are current research topics on MD simulation of DNA. Thanks.
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
This larva was captured using a plankton net in the Persian Gulf during the summer. I believe it may be a Facetotecta nauplius.
08 August 2024 3,746 4 View
May members post flyers about opportunities to present at a conferehttps://veraeducation.com/nce? If so, where to post for the Virginia Educational Research Association? https://veraeducation.com/
08 August 2024 4,585 1 View
If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...
07 August 2024 5,343 2 View
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
My name is Apurva Saoji. I am a Ph.D scholar in Computer engineering in India. I am looking for international expert in reviewing my PhD thesis, "Competitive Optimization Techniques to Minimize...
07 August 2024 4,600 2 View
Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...
07 August 2024 8,414 2 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
Please can anyone support with the survey questions based on RQ measures and propose how to do it in FMCG industry and include as well the role of brand equity Thanks
06 August 2024 949 0 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 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