AMBER Archive (2004)

Subject: Re: AMBER: Simulated annealing ...vlimit problem

From: anshul_at_imtech.res.in
Date: Sun May 16 2004 - 15:01:55 CDT

hi all,
yes like Venkati too am getting the same problem with the vlimit error,
but unfortunately not been able to solve it till now.

David a few days back you gave me the suggetsion of purtting the group
information at the end but that thing did not work but on the contrary if
i keep it in the begining it works. here is the input

Group input for restrained atoms (A1-A166)
 2 RES 1 167 END Group input for restrained atoms (A182-A276)
 2 RES 182 276 END END
 &cntrl
    imin=0, cut=30, nstlim=30000, ntt=1, ntx=1, irest=0,
    ntpr=200, ntwx=500, ntwe=500, tempi=10,
    ntb=0, ntr=1, dielc=4, vlimit=30, nmropt=1,
 &end
 &ewald
    eedmeth=5,
 &end
 &wt type='TEMP0', istep1=0,istep2=15000,value1=10.0,
           value2=500.0, &end
 &wt type='TEMP0', istep1=15001,istep2=20000,value1=500.0,
           value2=500.0, &end
 &wt type='TEMP0', istep1=20001,istep2=25000,value1=500.0,
           value2=300.0, &end
 &wt type='TEMP0', istep1=25001,istep2=30000,value1=300.0,
           value2=300.0, &end
 &wt type='TAUTP', istep1=0,istep2=20000,value1=1.0,
           value2=1.0 &end
 &wt type='TAUTP', istep1=20001,istep2=25000,value1=0.5,
           value2=0.5 &end
 &wt type='TAUTP', istep1=25001,istep2=30000,value1=0.2,
          value2=0.2 &end
 &wt type='END' &end

This way it reads all the given informatin (including th eedmeth flag
which was not read previously). but now there are two problems:

1) as given in the input file i want to raise the temp till 500K in the
first 15 ps but i am not able to reach this temperature. for this I
changed the tautp value. if i use a tighter coupling it seems to get
closer to the desired temperature. so i would like to know if this this
the correct procedure? does anyone have any related literature regarding
the correct use of tautp value?

2) my second problem is that the process is not completed and gives the
following error:

Frac coord min, max: 0.18535488200321256 1.0000102218677864
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

when initially the tautp value was higher (about 4) i got this error after
about 18 ps (when temperature rose to just 280K in 15 ps instead of 500K);
theni decreased tautp tp 2 and got the same error after 16ps (temperature
at 15 ps = 420K); finally i used tautp of 1.0 and got the error after 13.6
(with temperature of 400K at this stage).

So now can anyone solve these problems??

any help is greatly appriciated.

anshul

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