---
Dear All, I wonder what is the best choice for saving and storing trajectory files (dcd and ...) and all other sensitive and delicate items? any special brand of external hards? regards
02 March 2019 6,503 1 View
Hi all, I am trying to simulate a protein containing a modified Lysin : Trimethyllysine. I am a NAMD user and I couldn't find a proper forcefield (topology and parameter files) with charmm yet....
11 December 2018 7,202 9 View
Hi, I am working with NAMD but I need to know about gmx genrestr and isometric force constant. What that it mean? Is it like pulling and Steered molecular dynamics (SMD) in NAMD? Thank you in advance
09 October 2018 9,178 0 View
these two algorithms seems fast and efficient for aligning (superpose) two proteins: Acta Chrystallogr. Sect. A 61 (2005) 478 [doi: 10.1107/S0108767305015266] J. Comput. Chem. 31 (2010)...
08 September 2018 9,510 1 View
Hi, I need help with performing a simulation of a ligand and a protein. I am using psfgen code and add a ligand as the second segment but my parameter file couldnt recognize the new molecule...
08 September 2018 9,632 6 View
Dear All, According to VMD, two plug-in called Autoionize and Cionize are able to neutralize a normal system and highly charged system,respectively. In Gromacs we have only genion for both. Can...
06 July 2018 6,728 0 View
Hi everyone. I am new in the field of molecular dynamic. Would you please help me with altering large DCDs? I want to extract the C-alpha trajectory from my large dcd which is too large to be...
11 December 2017 7,946 6 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
I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...
02 March 2021 1,830 3 View
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
02 March 2021 4,569 4 View
Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...
02 March 2021 7,161 3 View
I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...
01 March 2021 3,610 1 View
01 March 2021 1,290 2 View
I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...
28 February 2021 4,966 3 View
I wanted to add an extra parameter to the existing Johnson cook equation in the ABAQUS simulation. How to add those extra parameters. Ref: A modified Johnson-Cook material model with strain...
28 February 2021 4,841 3 View
Hi, all! How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials? I have not find the choice for explicit element in Abaqus CAE. I am wondering whether it is possible...
25 February 2021 9,936 2 View
25 February 2021 5,713 1 View
