Hi
I have to impose a spherocylindrical confinement on the particles I am
currently performing simulation with.
For that I will appreciate your feedback/comments regarding two of my plans:
1. I was mainly looking at flat-bottomed potential option within gromacs
to see if it can be used to
Hi GROMACS users,
I solved my proteinin a defined box of water. Now I want to add ions to
neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro
-pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror :
Fatal error:No such moleculetypeSOLFor more informationand
Dear all
While calculating the diffusion constant using Green-Kubo equation using
the command : g_velacc -acflen 1001 -nonormalize -mol -n index.ndx -s
run.tpr followed by g_analyze -f vac.xvg -integrate we get three values as
average, standard deviation and SD sqrt(n-1).
Kindly tell me which of
Hi, I have run a REMD, which including 46 replicas. I searched how to analyze
my REMD statistics, but I am still confused how to analyze my result; how to
generate a continuous a energy distribution curve; how to deal with 46 .log
files. It seems so complicated.
one of my md.log file is as
