AMBER Archive (2005)

Subject: AMBER: Temperature regulation

From: Monica Civera (monica.civera_at_unimi.it)
Date: Tue Aug 30 2005 - 09:43:26 CDT

 
Dear all,

 

we perform MD simulation with AMBER 7.0 in NVT conditions at the unusually high temperature of 548 K. (see input below)

We notice that the average temperature during our 10 ns long run is around 564 +/- 4 K. It seems to be equilibrated but not around the selected value. The system, consisting of a 64-residues protein in TIP3P waters, was pre-equilibrated at 498 K. Higher temperature NTP simulations are not possible due to the breakdown of the entire system (evaporation?).

Could the problems be in the equilibration (than in the artificial density) or in the thermal bath coupling constant used?

 

 

Thanks in advance

Monica

 

 

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&cntrl

imin=0, ntx=5, irest=1, ntpr=500, ntwr=500, ntc=2,ntwx=500,

ntf=2, ntb=1, nstlim=100000, dt=0.001, ntt=1, cut=8,temp0 = 548.,

 tautp=2.0,taup=2.0

 &end

&ewald

use_pme=0,eedmeth=4

&end

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