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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Received on Sun Aug 27 2006 - 06:07:14 PDT
