AMBER Archive (2006)

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

From: Jardas sucuriba (jarda_s_at_hotmail.com)
Date: Fri Aug 25 2006 - 07:36:45 CDT


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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