Hi
Following are the last few steps from the out file. I ran with
taup=3....the error file shows "forrtl: severe (174): SIGSEGV,
segmentation fault occurred" ...
the logfile is empty and the outfile ends like this...
NSTEP = 60 TIME(PS) = 108.120 TEMP(K) = 310.94 PRESS = -456.1
Etot = -101537.0297 EKtot = 28047.0086 EPtot = -129584.0383
BOND = 9408.1729 ANGLE = 12092.3222 DIHED = 13740.7154
1-4 NB = 4267.7261 1-4 EEL = 44487.6913 VDWAALS = -6546.1751
EELEC = -207034.4910 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 3791.9870 VIRIAL = 6969.9047 VOLUME = 322692.0302
Density = 1.0543
Ewald error estimate: 0.9157E-04
------------------------------------------------------------------------------
NSTEP = 61 TIME(PS) = 108.122 TEMP(K) = 308.00 PRESS = -445.4
Etot = -101648.8565 EKtot = 27781.3979 EPtot = -129430.2545
BOND = 9540.3648 ANGLE = 12073.9388 DIHED = 13736.1957
1-4 NB = 4266.4631 1-4 EEL = 44500.4421 VDWAALS = -6540.6172
EELEC = -207007.0418 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 3794.4498 VIRIAL = 6897.6462 VOLUME = 322687.6443
Density = 1.0543
Ewald error estimate: 0.9566E-04
------------------------------------------------------------------------------
NSTEP = 62 TIME(PS) = 108.124 TEMP(K) = 306.65 PRESS = -421.3
Etot = -101576.6159 EKtot = 27659.5169 EPtot = -129236.1328
BOND = 9660.0967 ANGLE = 12125.4157 DIHED = 13735.8601
1-4 NB = 4267.2141 1-4 EEL = 44506.7052 VDWAALS = -6538.8386
EELEC = -206992.5861 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 3796.8207 VIRIAL = 6732.4106 VOLUME = 322683.3613
Density = 1.0543
Ewald error estimate: 0.9092E-04
------------------------------------------------------------------------------
NSTEP = 63 TIME(PS) = 108.126 TEMP(K) = 309.20 PRESS = -425.6
Etot = -101706.7723 EKtot = 27889.9176 EPtot = -129596.6899
BOND = 9226.7995 ANGLE = 12237.5482 DIHED = 13738.3250
1-4 NB = 4271.5460 1-4 EEL = 44507.0750 VDWAALS = -6539.0420
EELEC = -207038.9417 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 3798.4108 VIRIAL = 6763.6714 VOLUME = 322679.3091
Density = 1.0543
Ewald error estimate: 0.8888E-04
------------------------------------------------------------------------------
NSTEP = 64 TIME(PS) = 108.128 TEMP(K) = 321.03 PRESS = -428.1
Etot = -97513.2726 EKtot = 28956.4990 EPtot = -126469.7716
BOND = 9523.8510 ANGLE = 12367.5423 DIHED = 13740.9711
1-4 NB = 6506.2939 1-4 EEL = 44502.5072 VDWAALS = -6000.0603
EELEC = -207110.8767 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 3800.1819 VIRIAL = 6782.9405 VOLUME = 322675.2160
Density = 1.0543
Ewald error estimate: 0.8934E-04
------------------------------------------------------------------------------
NSTEP = 65 TIME(PS) = 108.130 TEMP(K) = 367.01 PRESS = -296.4
Etot = -95710.8501 EKtot = 33104.0082 EPtot = -128814.8584
BOND = 9975.8859 ANGLE = 12368.2107 DIHED = 13745.1684
1-4 NB = 4264.4563 1-4 EEL = 44498.8905 VDWAALS = -6497.0163
EELEC = -207170.4538 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 4300.1049 VIRIAL = 6365.3493 VOLUME = 322671.0988
Density = 1.0543
Ewald error estimate: 0.9319E-04
------------------------------------------------------------------------------
NSTEP = 66 TIME(PS) = 108.132 TEMP(K) = 345.96 PRESS = 208.5
Etot = -95848.2352 EKtot = 31205.2013 EPtot = -127053.4365
BOND = 11391.5055 ANGLE = 12346.5910 DIHED = 13751.9447
1-4 NB = 4261.2471 1-4 EEL = 44490.8138 VDWAALS = -6110.0303
EELEC = -207185.5083 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 4284.0995 VIRIAL = 2831.4120 VOLUME = 322668.2452
Density =
1.0543 Ewald error estimate: 0.9646E-04
------------------------------------------------------------------------------
NSTEP = 67 TIME(PS) = 108.134 TEMP(K) = NaN PRESS = 2389.8
Etot = NaN EKtot = NaN EPtot = -126024.2747
BOND = 11672.2387 ANGLE = 12373.5408 DIHED = 13757.5863
1-4 NB = 4266.1310 1-4 EEL = 44485.9585 VDWAALS = -5430.9609
EELEC = -207148.7692 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 4218.5489 VIRIAL = -12430.7877 VOLUME = 322670.2361
Density =
1.0543 Ewald error estimate: 0.1006E-03
The pressure has fallen so much in step 65...but i cannot see anything
unusual in the trajectory on vmd...
Thanks for your help
debostuti
On Thu, May 17, 2012 at 6:53 AM, case <case.biomaps.rutgers.edu> wrote:
>
> On Wed, May 16, 2012, DEBOSTUTI GHOSHDASTIDAR wrote:
> > >
> > > I am trying to equilibrate a system of DNA in Ionic liquids using
> > > Amber11/ff99bsc0. I have done several steps of heating and cooling,
> > > followed by stepwise heating in NVT. However the moment I start running NPT
> > > the system 's energy falls drastically and the run stops.
>
> Well, be sure to do the usual: set nstlim=50 or so and ntpr=1. Check the
> density and how it changes. Make sure that taup is large. Does the "run
> stop" with any messages at all? (I think you are saying "no", but your
> message was not very clear on this point.)
>
> ....dac
>
>
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Received on Sat May 19 2012 - 02:30:03 PDT
