I want to generate an infinite peptide fibril as has been mentioned in attached publication.
I am using gromacs but dont know which options to be used with -pbc option in .mdp file.
please help
Please help for setting up a dimeric peptide infinite only in z-direction with constant distance between periodic images in GROMACS. Thanks Lata
03 April 2018 5,190 4 View
Kindly suggest how to analyse H-bond between peptide and surrounding water molecules from a gromacs trajectory file.
04 May 2017 768 2 View
I want to perform calculation in solvent 2,2,2-Trifluoroethanol in gaussian but its not defined in gaussian. Please help me out how should I proceed for the same.
01 February 2017 5,540 5 View
Dear All, please let me know how to perform population analysis (Boltzmann distribution) from MD simulation (in terms of energy). I have Phi/ Psi dihedral values from MD simulations (Gromacs), I...
31 December 2016 210 4 View
How to generate a SER dipeptide with O-GlcNAc (beta- glucosamine) attachment at side chain with OH group of SER. I have genetared the dipeptide with O-GlcNAc , It shows complete dipeptide when...
04 May 2016 966 2 View
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
Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...
03 March 2021 5,999 3 View
Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...
28 February 2021 5,650 1 View
Hi, I'm looking for public datasets that have CT, X-ray information, or medical records for patients with Covid-19. Does anyone have suggestions?
28 February 2021 4,760 3 View
One of the publication I co-authored has the author's name in abbreviation. Then, somebody whose nothing to do with that paper acquired it as her work. To whom in this RG shall I ask for a hand,...
27 February 2021 4,206 4 View
I want to publish paper in journal but I have figures which have drawn with bio-renders, can I put them in the paper or which other software I can use to draw them?
27 February 2021 8,179 1 View
Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...
26 February 2021 10,014 3 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
25 February 2021 6,314 1 View
Hello, I created a profile for my friend on google scholar. I have added a verified email address. I marked the profile as public. Formerly his profile was visible. However, now, When I type his...
24 February 2021 8,680 3 View
During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...
23 February 2021 5,065 8 View