AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Aug 24 2006 - 11:24:28 CDT

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
>
>
>
>
>
>
> I am having the following error while running ptraj:
>
>
> Checking coordinates: md1.mdcrd
>
>> Checking coordinates: md2.mdcrd
>> Checking coordinates: contmd2.mdcrd
>>
>> ERROR in getArgumentDouble(): Scanning double precision argument failed
>> *** glibc detected *** double free or corruption: 0x080faf22 ***
>> *** glibc detected *** double free or corruption: 0x080faf22 ***
>>
>>
>> My input file is:
>>
>> trajin md1.mdcrd
>> trajin md2.mdcrd
>> trajin contmd2.mdcrd
>> center origin :1-256
>> image origin center familiar
>> atomicfluct out back_atomicflubyatom.apf @C,CA,N byatom
>> diffusion @CA time 0.2 CAtudo
>> solvent byname WAT TIP3
>> watershell :1-20 watwershellprotein.list
>> watershell :1 watershell1.list
>> watershell :2 watershell2.list
>> watershell :3 watershell3.list
>> watershell :4 watershell4.list
>> watershell :5 watershell5.list
>> watershell :6 watershell6.list
>> watershell :7 watershell7.list
>> watershell :8 watershell8.list
>> watershell :9 watershell9.list
>> watershell :10 watershell10.list
>> watershell :11 watershell11.list
>> watershell :12 watershell12.list
>> watershell :13 watershell13.list
>> watershell :14 watershell14.list
>> watershell :15 watershell15.list
>> watershell :16 watershell16.list
>> watershell :17 watershell17.list
>> watershell :18 watershell18.list
>> watershell :19 watershell19.list
>> watershell :20 watershell20.list
>> watershell :21 watershell21.list
>> watershell :22 watershell22.list
>> watershell :23 watershell23.list
>> watershell :24 watershell24.list
>> watershell :25 watershell25.list
>> watershell :26 watershell26.list
>> watershell :27 watershell27.list
>> watershell :28 watershell28.list
>> watershell :29 watershell29.list
>> watershell :30 watershell30.list
>> watershell :31 watershell31.list
>> watershell :32 watershell32.list
>> watershell :33 watershell33.list
>> watershell :34 watershell34.list
>> watershell :35 watershell35.list
>> watershell :36 watershell36.list
>> watershell :37 watershell37.list
>> watershell :38 watershell38.list
>> watershell :39 watershell39.list
>> watershell :40 watershell40.list
>>
>>
>> Does anyone know what is happening? Is there anything wrong with this
>> script?
>>
>> Thanks in advance
>> Jardas
>>
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