8 Questions 20 Answers 0 Followers
Questions related from Farzane Jalalypour
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
03 March 2019 6,572 1 View
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02 February 2019 7,846 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....
12 December 2018 7,266 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
10 October 2018 9,264 0 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...
09 September 2018 9,694 6 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)...
09 September 2018 9,592 1 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...
07 July 2018 6,817 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...
12 December 2017 8,055 6 View
