AMBER Archive (2003)

Subject: virtual box

From: eric hu (erichu_linux_at_yahoo.com)
Date: Tue Jan 07 2003 - 17:26:15 CST

Hi I'm running md with NMR bond restraints. Amber 7
stops after 14ps with the following message.
Interestingly, when I restart the job from the rst
file, amber stops at 35ps with the same effor message.
Is there a way the amber can recalculate the virtual
box periodically? Thanks. -Eric

 Frac coord min, max: 8.23603576138125D-002
1.00001202699347
 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

Input:
MD in-vacuo
 &cntrl
   irest=0, ntr=1,
   igb = 0, ntb = 0, ntpr = 100, ntwx = 10,
   cut = 10.0, nmropt=1,
   tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
   imin = 0,vlimit=10
   nstlim = 100000, dt = 0.001,
 &end
 &wt type='REST', istep1=0,istep2=0,value1=1.0,
    value2=1.0,
 &end
 &wt type='END'
 &end
DISANG=./DISANG
LISTOUT=POUT
END
END

DISANG:
 &rst
    iat=1,1, nstep1=1,nstep2=10000,
   
iresid=1,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
    atnam='O04','C05',
    r1=0.00000E+00,r2=2.130,r3=2.130,r4=5.00,
       rk2=9999.0,rk3=9999.0,
    r1a=0.00000E+00,r2a=2.130,r3a=2.130,r4a=5.00,
       rk2a=9999.0,rk3a=9999.0,
 &end
 &rst
    iat=1,1, nstep1=1,nstep2=10000,
   
iresid=1,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
    atnam='C01','C18',
    r1=0.00000E+00,r2=2.04,r3=2.04,r4=5.00,
       rk2=9999.0,rk3=9999.0,
    r1a=0.00000E+00,r2a=2.04,r3a=2.04,r4a=5.00,
       rk2a=9999.0,rk3a=9999.0,
 &end

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