Thank you for advice, Guanglei.
Indeed, I make a mistake for the expression of MD equilibration and
minimisation. Because the PC computers didn't work well, the MD calculation
was stopped. The following is the last part of the out file:
>> ..........
>> check COM velocity, temp: 0.000000 0.00(Removed)
>>
>> NSTEP = 243000 TIME(PS) = 343.000 TEMP(K) = 298.07 PRESS = 74.2
>> Etot = -135776.3955 EKtot = 34230.4686 EPtot = -170006.8641
>> BOND = 1390.9959 ANGLE = 3840.7207 DIHED = 2831.0646
>> 1-4 NB = 1771.5752 1-4 EEL = 19298.0512 VDWAALS = 18423.3245
>> EELEC = -217562.5961 EHBOND = 0.0000 RESTRAINT = 0.0000
>> EKCMT = 14257.9496 VIRIAL = 13364.8005 VOLUME = 557721.5180
>> Density = 1.0248
>> Ewald error estimate: 0.4038E-04
>> -------------------------------------------------------------------------
>>
>>
>> -- ---
>>
>>
>> NSTEP = 243500 TIME(PS) = 343.500 TEMP(K) = 299.46 PRESS = -25.6
>> Etot = -135772.9031 EKtot = 34390.5275 EPtot = -170163.4306
>> BOND = 1333.4578 ANGLE = 3779.1680 DIHED = 2811.4527
>> 1-4 NB = 1778.6720 1-4 EEL = 19250.4781 VDWAALS = 18629.4244
>> EELEC = -217746.0836 EHBOND = 0.0000 RESTRAINT = 0.0000
>> EKCMT = 14448.9849 VIRIAL = 14756.8950 VOLUME = 557481.1031
>> Density = 1.0253
>> Ewald error estimate: 0.2375E-04
>> -------------------------------------------------------------------------
>>
>>
>> -- ---
>>
>> check COM velocity, temp: 0.000000 0.00(Removed)
>>
>> NSTEP = 244000 TIME(PS) = 344.000 TEMP(K) = 299.42 PRESS = 9.6
>> Etot = -135758.2209 EKtot = 34385.2687 EPtot = -170143.4896
>> BOND = 1387.1727 ANGLE = 3755.3665 DIHED = 2835.6052
>> 1-4 NB = 1766.1725 1-4 EEL = 19358.7201 VDWAALS = 18301.0670
>> EELEC = -217547.5935 EHBOND = 0.0000 RESTRAINT = 0.0000
>> EKCMT = 14512.6075 VIRIAL = 14397.3689 VOLUME = 558003.0154
>> Density = 1.0243
>> Ewald error estimate: 0.2324E-05
>> -------------------------------------------------------------------------
>>
>>
Unfortunately, the restart file wasn't written when the job was teminated.
So I use the ptraj input/output commands to creat the restart file of the
last frame. Then continue running the MD equilibration in the constant
temprature with amber7. The input file is &cntrl
nstlim=500000, dt=0.001, ntx=5, irest=1, ntpr=500, ntwr=500, ntwx=500,
tempi=298.15, temp0=298.15,
ntt=1, tautp=2.0,
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
cut = 10.0,
&end
But the restart MD calculation can't work well. The error as the
following:
---------------------------------------------------
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
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 20197851
| TOTAL SIZE OF NONBOND LIST = 20197851
vlimit exceeded for step 0 ; vmax = Infinity
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 103 182 183
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
----------------------------------------------------------------------------
I have checked the restart file created from the last frame by the ptraj
input/output commands, it
seems it is OK, but the MD restarting calculation is still unsuccessful.
What should I do to deal with this problem?
Thank you again.
On Mon, 25 Apr 2005 10:37:50 -0400, Guanglei Cui <cuigl.csb.sunysb.edu>
wrote:
> Hi,
>
> You should try to do the minimization with no SHAKE. And what do you mean
> by "net transmission"? The input file you gave looks to me a MD input. MD
> and minimization are two different options set by imin flag. The default
> is imin=0, which is MD. I suggest you take a look at AMBER tutorial page
> for examples of running sander or perhaps the book by Andrew Leach
> "Molecular Modeling:...".
>
> Good luck.
>
> Guanglei
>
>>
>>
>> What can I do to deal with this problem?
>> Thank you for help in advance.
>>
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Received on Tue Apr 26 2005 - 12:53:00 PDT
