Hi
>Look at the components of the energy at this step. Compare them to the
>individual components of step "0" in your MD run. Report any differences.
I did it. Few components are different:
Min.
NSTEP ENERGY RMS GMAX NAME NUMBER
2500 -1.0766E+05 7.5114E-01 7.8713E+01 C6 3838
BOND = 7906.5852 ANGLE = 529.6831 DIHED = 2310.5740
VDWAALS = 19126.7051 EEL = -147423.9068 HBOND = 0.0000
1-4 VDW = 822.2452 1-4 EEL = 8936.0878 RESTRAINT = 134.0700
EAMBER = -107792.0264
MD
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 438.35 PRESS = 0.0
Etot = -89978.9428 EKtot = 25598.9152 EPtot = -115577.8580
BOND = 120.7537 ANGLE = 529.6831 DIHED = 2310.5740
1-4 NB = 822.2452 1-4 EEL = 8936.0877 VDWAALS = 19126.7051
EELEC = -147423.9068 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.1085E-03
I think that the RESTRAINT component should not be 0.0 at the step 0 of MD. Could this cause a problem during the MD?
>What are your starting velocities? You have a temperature of 508K at step
>2 of the MD run. And you already have potential energy that is 10,000
>kcal/mol higher than in the minimization. You need to try to track down
>where such difference are coming from.
The input file for the MD was:
&cntrl
imin=0,
irest=0,
ntx=1,
ig=-1,
ntb=1,
ntr=1,
cut=10,
ntc=2,
ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,
gamma_ln=5.0,
nstlim=15000, dt=0.001,
ntpr=1, ntwx=1, ntwr=1000
restraint_wt = 10.0,
restraintmask=':1-246.CA,C,O,N | .3834-3843'
Since I want to relax in a NVT ensemble solvent molecules of the structure previously minimized, might be more correct set irest=1 and ntx=7?
Vale
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 15 2014 - 06:30:02 PDT
