My problem of today is my NVT MDsimulation with GB/SA conditions.
The simulations starts, but I don't receive any values for my Egb or Esasa in my E.dat output file. They are always 0.0000 for every times step.
Here is the input file I used. Just have a look and tell me if I make any critical mistakes.
Another problem came up, when I wanted to use cutoff values in my simulation. If I do so, the simulation stop's immediately and prints the following line in the log.txt :
"Error: unknown input command: cutoff [A] 14.0"
Here is the hippo_input.txt I use:
hippo input file
mode MD simulation
input type [PDB,zmx] PDB
input file minimized.pdb
random number seed (must be < 0) -100
T [K] 298.15
use_SSE (0 = slow double prec.) 1
united atom for aliphatic C 0
r_probe [A] 1.4
intra molecule epsilon 1.0
use_gb_flex123 (flexible 1-2 1-3) 0
MD timestep [fs] 0.5
use rattle for H bonds 0
Collision frequency [steps] 500
Collision ratio [of all atoms] 0.05
openMP numthreads 4
Discussions on how to set up simulations, typically starting from a pdb file.
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