Problem with Hippo_input setup for GB/SA

Discussions on how to set up simulations, typically starting from a pdb file.
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m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Problem with Hippo_input setup for GB/SA

Post by m.kalavera » Wed Feb 25, 2009 11:48 am

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
use_pdb_coordinates 1
max_steps 5000000
T [K] 298.15
use_SSE (0 = slow double prec.) 1
use_pbc 0
match_hydrogens 1
freq_pdb_out 1e2
freq_xyz_out 1e4
freq_E_out 1e2
freq_state_restart_out 1e5
print_speed 1
print_debug 1
use_gbsa 1
gb_mode 2
united atom for aliphatic C 0
r_probe [A] 1.4
sigma 0.005
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
thermostat 1
Collision frequency [steps] 500
Collision ratio [of all atoms] 0.05
use_NPT 0
openMP numthreads 4

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Re: Problem with Hippo_input setup for GB/SA

Post by m.kalavera » Thu Feb 26, 2009 3:53 pm

I solved my problem,
the entry "use_SSE (0 = slow double prec.) 1" has to be changed to zero instead of one.

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