AMBER Archive (2006)

Subject: Re: AMBER: missing values in md.out

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Aug 25 2006 - 07:53:26 CDT

it is possible to write restart files at different intervals than the
mdout output.
restart interval is set by ntwr, mdout is set by ntpr. if these are not
the same then
it might not match. Another possibility is as you say the job did not
complete
properly, so it is hard to say whether the last frame will be written or
not.
see if you have ntpr and ntwr set to the same values. also set ntwx to a
small enough
value that the job won't' crash from filesize limits (or use larger ntwx).

Jardas sucuriba wrote:

> Hi
>
> I used ntpr=100, dt=0.002. My system is large and the MD stopped for
> three times because the trajectory file reached the 2 Gb (I just
> understood that later). I always continued the simulation until the
> 1050 ps and I obtained four md.out files for the production phase.
>
> Here is the end of my first md.out file after the equilibration phase:
>
> NSTEP = 153700 TIME(PS) = 357.400 TEMP(K) = 301.22 PRESS
> = 289.9
> Etot = -125690.1365 EKtot = 36701.8962 EPtot =
> -162392.0328
> BOND = 3045.5291 ANGLE = 8013.4165 DIHED =
> 10237.0700
> 1-4 NB = 3639.9303 1-4 EEL = 39118.6308 VDWAALS =
> 10395.8087
> EELEC = -236842.4181 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> EKCMT = 12750.9827 VIRIAL = 9221.3459 VOLUME =
> 563822.4436
> Density
> = 1.0653
> Ewald error estimate: 0.9745E-04
> ------------------------------------------------------------------------------
>
>
>
> Here is the begining of my second md.out file:
>
> 4. RESULTS
> --------------------------------------------------------------------------------
>
>
> ---------------------------------------------------
> 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 = 0.2763E-14 at 2.626100
> | CHECK d/dx switch(x): max rel err = 0.7525E-11 at 2.750640
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 21076603
> | TOTAL SIZE OF NONBOND LIST = 21076603
>
> NSTEP = 100 TIME(PS) = 357.200 TEMP(K) = 298.72 PRESS
> = 61.3
> Etot = -126046.2420 EKtot = 36398.1115 EPtot =
> -162444.3535
> BOND = 2931.8037 ANGLE = 8070.9083 DIHED =
> 10209.9273
> 1-4 NB = 3635.3813 1-4 EEL = 39059.0277 VDWAALS =
> 10066.6303
> EELEC = -236418.0322 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> EKCMT = 12579.0345 VIRIAL = 11833.2190 VOLUME =
> 563547.1785
> Density
> = 1.0658
> Ewald error estimate: 0.5014E-04
> ------------------------------------------------------------------------------
>
>
>
> I think strange that the second md.out file had started at 357.200 ps
> and not at 357.400 ps. This also happened with the other md.out files.
> Is it possible that the MD interruptions had caused the corruption of
> the restarted md.out files but not the trajectory files? So, when a
> MD stop, because of an energy failure or because the trajectory file
> has reached the size limit, is it safe to continued it or is it better
> to restart it again? Is there any test that I can do to see if my
> files are corrupted?
>
>
>
>> From: Carlos Simmerling <carlos_at_csb.sunysb.edu>
>> Reply-To: amber_at_scripps.edu
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: missing values in md.out
>> Date: Thu, 24 Aug 2006 12:24:28 -0400
>>
>> what is the value of NTPR that you used?
>>
>>
>>
>> Jardas sucuriba wrote:
>>
>>> Dear amber users,
>>>
>>> I ran an MD simulation of 1050 ps (5250 frames). But the system
>>> properties of the last steps are not written to the md.out file.
>>> That is, the md.out ends in this way:
>>>
>>> NSTEP = 38900 TIME(PS) = 1048.800 TEMP(K) = 300.02 PRESS
>>> = 1.5
>>> Etot = -125834.1926 EKtot = 36556.5512 EPtot =
>>> -162390.7438
>>> BOND = 2978.9299 ANGLE = 7895.2012 DIHED =
>>> 10203.3897
>>> 1-4 NB = 3653.9454 1-4 EEL = 39141.8125 VDWAALS =
>>> 9957.9115
>>> EELEC = -236221.9340 EHBOND = 0.0000 RESTRAINT
>>> = 0.0000
>>> EKCMT = 12562.0090 VIRIAL = 12543.2915 VOLUME =
>>> 564194.9017
>>> Density
>>> = 1.0646
>>> Ewald error estimate: 0.4840E-04
>>> ------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> R M S F L U C T U A T I O N S
>>>
>>>
>>> NSTEP = 38900 TIME(PS) = 1048.800 TEMP(K) = 1.21 PRESS
>>> = 140.7
>>> Etot = 251.6377 EKtot = 147.8055 EPtot
>>> = 199.7428
>>> BOND = 46.5593 ANGLE = 69.2074 DIHED
>>> = 38.8728
>>> 1-4 NB = 26.0302 1-4 EEL = 71.5063 VDWAALS
>>> = 171.3676
>>> EELEC = 278.8712 EHBOND = 0.0000 RESTRAINT
>>> = 0.0000
>>> EKCMT = 84.8505 VIRIAL = 1720.5340 VOLUME
>>> = 448.8528
>>> Density
>>> = 0.0008
>>> Ewald error estimate: 0.3459E-04
>>> ------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> However the strange is that the trajectory contains all the 5250
>>> frames and for instance, if I compute the RMSD for the protein I
>>> obtain values for all the simulation steps.
>>>
>>> Does anyone experienced this before or have an idea of why my md.out
>>> file miss the values for the last ps? Does this mean that there is
>>> anyhing wrong with my md simulation?
>>>
>>> Thanks in advance
>>> Jardas
>>>
>>>
>>>
>>>
>>>
>>>
>
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