8 Questions 21 Answers 0 Followers
Questions related from Batsaikhan Mijiddorj
During the nvt it was okay. After the NVT equilibration, short NPT equilibration was performed. During this equilibration, free space generated inside box. Please tell me some possible reasons?
10 October 2018 8,615 0 View
Dear GMX experts, A simulation system consists of several peptide chains, and I would like to compare contacts of hydrophobic and electrostatic interaction. How can I estimate hydrophobic...
04 April 2018 9,878 3 View
Dear Experts, I generated LIG.str file using CGenFF for a specific molecule. I would like to use GROMACS package. I tried to convert LIG.str file to LIG.itp file. I tried as following command...
01 January 2018 9,446 3 View
Hello, I am very new user of Gaussian. I started the optimization of the connected two amino acids. Calculation was finished, and I would like to get the optimized structure. How can I know...
06 June 2017 7,156 5 View
Dear all, Hello, I have a 3D helical data consist of 40 points. I calculated SVD() using matlab, and I have got values (110, 10, 10). I understood that 110 is a dimension of the most variation...
02 February 2016 8,452 0 View
Hello, I want to represent some protein structures with vectors? Thank you, Mijiddorj
02 February 2016 3,434 1 View
Hello, I want to make pH dependent simulation of dimer, trimer and pentamer structure of peptide. How to make it using AMBER or GROMACS? Can I use H++ server for oligomers? or How to set manually....
01 January 2016 851 2 View
Hello, I have got following error during MMPBSA.py calculation for PBSA MD simulation. How to fix it? ******************************************************************** Beginning GB calculations...
11 November 2015 10,145 2 View
