Dear amber users,
I am using Amber16 to do a simulation for a complex. I first performed minimizations for the complex and everything is OK. However, when I want to equilibrate the water molecules and elevate the temperature of the system, the simulation can not proceed normally. There is no error information in the output file, but the simulation can not go on. Can any one help me?
The script is as follows:
$DO_PARALLEL sander.MPI -O -i mdw.in -o mdw.out -p 4NRE_solv.prmtop -c m4.rst -r mdw.rst -x mdw.mdcrd -ref m4.rst
The mdw.in file is as follows:
# Control section
&cntrl
nstlim=100000, dt=0.002, ntx=1, irest=0,ig=-1, ntpr=1000, ntwr=1000,ntwx=1000,
tempi=10.15, temp0=298.15, ntt=1,tautp=2,
ntb=1, ntp=0,
ntc=2, ntf=2,
cut=10.0,
ntr=1, restraintmask=':1-675',
restraint_wt=5.0,
&end
&ewald
&end
The mdw.out file is as follows and there is no error information.
***************
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 194726.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 194726. NUM_NOSHAKE = 0 CORRECTED RNDFP = 194726.
| TOTAL # of degrees of freedom (RNDF) = 194726.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
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Received on Thu Jul 21 2016 - 05:00:02 PDT
