12 Questions 7 Answers 0 Followers
Questions related from Amnah Alalmaie
Hello How to perform community network analysis using GROMACS trajectory Thank you so much
21 December 2022 721 0 View
Dear all, The complex I am trying to simulate has protein ( 10 chains), DNA, and RNA I ran the simulation for 2 us so far but the biological event I want to observe requires a very long MD...
02 June 2021 1,530 1 View
Hi I would like to MD simulate a CRISPR cryo-EM- structure. But only a small region of the R-loop was observed. I want to simulate the R-loop formation. How to model the missing part of the...
22 February 2021 6,007 0 View
Hi all I used the following script to run the simulation but for some reason, I was not able to assign GPU to do the PME calculation? How to do that? The size of the system is huge (600.000...
15 January 2021 7,587 1 View
Hi My system I am trying to simulate has 600.000 atoms. I want to simulate for 1 us I am using a supercomputer to run the simulation with tesla K80 GPUs. I am using 1 node and a total of 28 core...
09 January 2021 4,830 1 View
How to add a new termini database entries in amber FF for phosphorylated at 5'- and 3'-termini of DNA? Pdb2gmx is not able to covert pdb to gro files could you please help me?
23 September 2020 8,493 7 View
hello Is polyethlene glycol ( 5000 D) soluble in aceton and ethanol?
13 November 2018 2,177 1 View
PEG does not have chromophore do you know how to add a chromphore to make it detectable by UV detector? what is the chemistry behind that can anyone help me with that thank you
11 November 2018 4,701 1 View
11 November 2018 9,551 1 View
could you please provide me with some articles that done experiments on mice by using plain Gelatin? I want to study the effect of plain gelatin on mice
10 October 2018 9,438 0 View
Hello The standard time in our lab is 4 hrs for MCF-7 but the goal of my experiment is to study the effect of assay? The standard time in our lab is 4 hrs for MCF-7 but the goal of my...
04 April 2018 3,824 4 View
Dear all, I use Gromacs, and I got the following error. group Protein_chain_A referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or...
01 January 1970 4,497 3 View
