Hello, Amber Users!
I have a problem with my system. It's a small globular protein (286 aa).
When I was doing short simulations (10 ns) there was no problem, but right
now, when I want to do 50 ns simulations (5 x 10 ns) I see there is
something wrong with the system.
The volume is getting smaller, density is increasing and the total energy
is decreasing very fast. I'm using iwrap, so I grep some informations about
the water box size, and this is my output:
first 10 lines:
wrapping first mol.: -72.25756 0.00000 0.00000
wrapping first mol.: -72.25756 0.00000 0.00000
wrapping first mol.: -72.32379 0.00000 0.00000
wrapping first mol.: -72.32379 0.00000 0.00000
wrapping first mol.: -72.27254 0.00000 0.00000
wrapping first mol.: -72.27254 0.00000 0.00000
wrapping first mol.: -72.29022 0.00000 0.00000
wrapping first mol.: -72.29022 0.00000 0.00000
wrapping first mol.: -72.26856 0.00000 0.00000
wrapping first mol.: -72.26856 0.00000 0.00000
last 10 lines:
wrapping first mol.: -192.79918 -68.16483 -472.25958
wrapping first mol.: -192.79918 -68.16483 -472.25958
wrapping first mol.: -192.78991 -68.16155 -472.23687
wrapping first mol.: -192.78991 -68.16155 -472.23687
wrapping first mol.: -192.76965 -68.15439 -472.18724
wrapping first mol.: -192.76965 -68.15439 -472.18724
wrapping first mol.: -192.78179 -68.15868 -472.21697
wrapping first mol.: -192.78179 -68.15868 -472.21697
wrapping first mol.: -192.81269 -68.16961 -472.29267
wrapping first mol.: -192.81269 -68.16961 -472.29267
For the file preparation I'm using this procedure:
source leaprc.ff14SB
loadAmberParams frcmod.ionsjc_tip3p
solute = loadpdb protein.pdb
solvent = loadpdb wat.pdb
complex = combine {solute solvent}
solvateoct complex TIP3PBOX 10
addions complex Na+ 0
savepdb complex protien_complex.pdb
saveamberparm complex protein_complex.prmtop protein_complex.inpcrd
quit
And here is the production script:
# 5 ns production Langevin dynamics
&cntrl
imin=0,
irest=1, ntx=5,
ntpr=500, ntwx=500, ntwr=500,
ntb=2, cut=10, nsnb=10, iwrap=1,
nstlim=5000000, nscm=0, dt=0.002,
ntt=1, temp0=300, tempi=300, ig=-1,
ntp=1,
ntc=2, ntf=2,
/
What could be the problem here?
I was doing simulations using the same scripts, but with bigger molecules,
and there was no such problem. Please, help!
Best regards,
Karolina Markowska
PhD student
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Received on Mon Oct 19 2015 - 05:00:03 PDT
