AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem

From: praveena moldy <>
Date: Mon, 28 Feb 2005 05:36:36 +0000 (GMT)

Hello Amber Group,
       I want to run Poisson-Botzmann MD in NVE ensemble for a small peptide Ace-Ala3-NMe with the length of all bonds fixed. I have to equilibrate it to 300K slowly within 100ps.The time step of the simulaiton which I kept is 1fs. In the first 65ps the molecule is made to heat gradually to 300K, and in the successive 25ps the temperature is restrained to 300K and no temperature scaling is adopted in the successive 10ps.
The input I have used is the one below,
 cut=12.0, igb=10,
 temp0=300.0, tempi=0.0,
 type='TEMP0', istep1=0, istep2=65000,
        value1=0.0, value2=300.0,
 type='TEMP0', istep1=66000, istep2=90000,
        value1=300.0, value2=300.0,
hold peptide fixed
RES 1 42

While equilibrating the molecule, I got something like (after 0.15ps),
vlimit exceeded for step 157 ; vmax = 5540034186820002.
vlimit exceeded for step 158 ; vmax = 5.4060661364929577E+18
vlimit exceeded for step 159 ; vmax = 5.1700189427506561E+19
vlimit exceeded for step 160 ; vmax = 2.84653933347553812E+19
vlimit exceeded for step 161 ; vmax = 3.85341586976328188E+20
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!..........
and this has been continued till 3.4ps and the equilibration stops with the message,
vlimit exceeded for step 3400 ; vmax = 47.43705100474962
 vlimit exceeded for step 3401 ; vmax = 139.07727246991954
 vlimit exceeded for step 3402 ; vmax = 33.706126147486799
 vlimit exceeded for step 3403 ; vmax = 65.636635184900626
 vlimit exceeded for step 3404 ; vmax = 31.068175282916044
 vlimit exceeded for step 3405 ; vmax = 40.0656845829796
 vlimit exceeded for step 3406 ; vmax = 92.181793757499122
 vlimit exceeded for step 3407 ; vmax = 31.354599848532565
 vlimit exceeded for step 3408 ; vmax = 33.413529233998702
 vlimit exceeded for step 3409 ; vmax = 29.615107718328723
 vlimit exceeded for step 3410 ; vmax = 25.571031269519956
 vlimit exceeded for step 3411 ; vmax = 26.054697642189538
 vlimit exceeded for step 3412 ; vmax = 22.508337242911296
 Frac coord min, max: -9.84445917080887817E-4, 0.52496741432105076
 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.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

I do not know what went wrong. Is there any misatake in the input given.Could somebody help me regarding this.
Suggest me an idea to rectify this error.
Thank you,

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Received on Mon Feb 28 2005 - 05:53:00 PST
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