Try warming slowly. Equilibration should be covered in the demos.
Bill
On 6/25/16 6:03 AM, Shilpa Gupta wrote:
> Dear AMBER users,
> I am trying to create a acetone solvent box for my simulation. For this i have taken acetone solvent coordinates from REDDB and created acetone box in leap.Then i minimized this box.After this step heating, equilibration step is to be formed for which i have given the following input .
>
>
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> ntb=1,
> cut=9,
> ntr=0,
> ntc=1,
> ntf=1,
> tempi=0.0,
> temp0=300.0,
> ntt=3,
> gamma_ln=1.0,
> nstlim=1000,
> dt=0.001,
> ntpr=200,
> ntwx=200,
> /
> and with this input i got following output
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -20853.7885 EKtot = 0.0000 EPtot = -20853.7885
> BOND = 11.6469 ANGLE = 128.6183 DIHED = 32.7139
> 1-4 NB = 354.5842 1-4 EEL = -22758.3077 VDWAALS = -1526.6470
> EELEC = 2903.6030 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.1515E-01
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 1; vmax = 68.2747
> vlimit exceeded for step 2; vmax = 57.2000
> vlimit exceeded for step 3; vmax = 25.1653
> vlimit exceeded for step 4; vmax = 22.6759
> vlimit exceeded for step 5; vmax = 25.2932
> vlimit exceeded for step 6; vmax = **********
> vlimit exceeded for step 7; vmax = **********
> vlimit exceeded for step 8; vmax = 25179.0320
> vlimit exceeded for step 9; vmax = 574.8981
> vlimit exceeded for step 10; vmax = 396.5358
> vlimit exceeded for step 11; vmax = 615.9488
>
> and if i switch on shake with the following input
> &cntrl
> ntx=1,
> irest=0,
> ntpr=100,
> ntwx=500,
> ntf=2,
> ntb=2,
> cut=9.0,
> imin=0,
> nstlim=25000,
> dt=0.001,
> temp0=300.0,
> tempi=100.0,
> ntt=1,
> tautp=0.2,
> vlimit=15.0,
> ntp=1,
> pres0=1.0,
> comp=44.6,
> taup=0.2,
> ntc=2,
> /
>
> then output is coming out to be as follows
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 126.38 PRESS = -3377.7
> Etot = -19344.2959 EKtot = 1509.4926 EPtot = -20853.7885
> BOND = 11.6469 ANGLE = 128.6183 DIHED = 32.7139
> 1-4 NB = 354.5842 1-4 EEL = -22758.3077 VDWAALS = -1526.6470
> EELEC = 2903.6030 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 149.1591 VIRIAL = 5131.5274 VOLUME = 68317.4576
> Density = 0.7073
> Ewald error estimate: 0.1515E-01
> ------------------------------------------------------------------------------
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 4 1186 1971 1972
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> I could not able to diagnose the problem.can anyone help me on this.
> Thanks in advance.
>
>
>
> Shilpa Gupta
>
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Received on Sat Jun 25 2016 - 06:30:03 PDT
