That means there is no direct way to find out this using gromacs..
-- Origin message --
>From："Александр Лашков"
>To：gmx-us...@gromacs.org
>Subject：Re: [gmx-users] No.of ethanol molecules passing
>Date：2019-12-26 14:34:29For example: convert trajectory
For example: convert trajectory in text file format (.gro or .pdb), then
write a simple script (python, perl) for calculation,
Alexander
чт, 26 дек. 2019 г. в 09:23, Ali Ahmad (阿力) :
> Hi Groamcs Community
> I am a beginner in gromacs and my work area is pervaporative membrane
> simulation.
>
Hi Groamcs Community
I am a beginner in gromacs and my work area is pervaporative membrane
simulation.
My queries are
1: How to calculate that how many number of "X" molecules (in my case is
ethanol) passed through the membrane for certain period of time i.e 1000ps ?
from this a graph between
It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You
Hi,
i am trying to make the index file without loops and termini and using the
option protein and ligand that is 1 and 13 but the index file is formed
with the same as it is formed from the whole system.
--
Kind Regards
Nupur Munjal
PhD Scholar (Bioinformatics)
Department of Biotechnology &
See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838431/
ср, 25 дек. 2019 г. в 11:06, Shradheya R.R. Gupta :
> Hi,
> I encountered a problem during binding free energy calculation, as my
> ligand and protein is charged, periodic boundary conditions will introduce
> large artifacts. Is there a
Hi,
I encountered a problem during binding free energy calculation, as my
ligand and protein is charged, periodic boundary conditions will introduce
large artifacts. Is there a way or tutorial to correct this.
Thank you,
Shradheya Gupta
DBT-BIF University of Rajasthan
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