AMBER Archive (2007)

Subject: AMBER: Error when doing a TI simulation: "vlimit exceeded

From: ming hui (yongminghui_at_gmail.com)
Date: Wed Nov 14 2007 - 19:10:07 CST

Dear Amber users,

Currently I am investigating the binding of Tris to a protein, which may
also involve a water molecule mediating interactions, and I am performing 3
sets of TI simulations on Amber 8 where I make 1) Tris 2) the water
molecule 3) both Tris and the water molecule 'disappear'. For each value of
clambda, I perform an equilibration followed by production run at *300K*. For
the 2nd and 3rd set of simulations *only*, I occassionally encounter the
following problem in my simulations:
e.g.

vlimit exceeded for step 28 ; vmax = 21.702316513373937

vlimit exceeded for step 29 ; vmax = 32.04395996859634

vlimit exceeded for step 30 ; vmax = 23.300233582359617

At some point it even caused one of my simulations to stop completely.

When I looked at the energetics, I noticed that except for the very first
simulation (equilibration for clambda=0), the total energy of the system
would be less negative at the beginning (aobut -50 000) perhaps due to the
high temperature/velocities? and then gradually decrease to the normal value
of about -58000:

beginning of simulation:

 NSTEP = 1000 TIME(PS) = 10531.000 TEMP(K) = *363.43
* PRESS = 124.2
 Etot = -50007.0391 EKtot = 17518.9795 EPtot = -
67526.0186
 BOND = 710.7133 ANGLE = 1866.7031 DIHED =
1982.2596
 1-4 NB = 685.9417 1-4 EEL = 5936.5945 VDWAALS =
7349.9654
 EELEC = -86163.5183 EHBOND = 0.0000 RESTRAINT =
105.3222
 EAMBER (non-restraint) = -67631.3407
 DV/DL = 12.3382
 EKCMT = 7286.6027 VIRIAL = 6619.1947 VOLUME =
248973.3195
                                                    Density =
0.9670
---------------------------------------------------------------------------------------------------------------------------------------------------------------

end of simulation:

 NSTEP = 50000 TIME(PS) = 10580.000 TEMP(K) =
298.49
 PRESS = 51.0
 Etot = -58287.5803 EKtot = 14388.5223 EPtot = -
72676.1026
 BOND = 564.6240 ANGLE = 1525.1773 DIHED =
1811.2377
 1-4 NB = 665.5837 1-4 EEL = 6000.8952 VDWAALS =
8044.5602
 EELEC = -91329.3281 EHBOND = 0.0000 RESTRAINT =
41.1473
 EAMBER (non-restraint) = -72717.2500
 DV/DL = 13.0097
 EKCMT = 6124.9146 VIRIAL = 5866.5524 VOLUME =
234643.1241
                                                    Density =
1.0261
 Ewald error estimate: 0.7278E-04
---------------------------------------------------------------------------------------------------------------------------------------------------------------

My input file for all the simulations (and for every set 1)-3)) (with only
clambda varied) is as follows (my TI involves restraining the atom
'disappearing', however due to rotation of the protein and other ligand I
also restrain some of the main chain atoms and that ligand):

 &cntrl

  imin = 0, irest = 1, ntx = 7,

  ntb = 2, pres0 = 1.0, ntp = 1,

  iwrap = 1,

  igb = 0,

  ntave = 5000,

  cut = 12,

  ntr = 1,

  ntc = 2, ntf = 2,

  tempi = 300.0, temp0 = 300.0,

  ntt = 3, gamma_ln = 1.0,

  nstlim = 100000, dt = 0.001,

  ntpr = 1000, ntwr = 1000,

  icfe = 1, clambda = 0.00

 /

Hold O atom of w6280

4.62

ATOM 21202

END

Hold central C atom of tris

1.96

ATOM 2925

END

Hold mainchain atoms of residues within 15 A of tris

2

FIND

* * M *

SEARCH

RES 1 19

… …

END

END

---------------------------------------------------------------------------------------------------------------------------------------------------------------

I would really appreciate any advice on what could be causing the problem
and how to overcome it. As mentioned before, the thing is that the problem
only arose when I tried to make the TIP3 water molecule (alone or together
with Tris) disappear (there were no problems 'disappearing' it from a bulk
solution of only water molecules). The Tris molecule is charged, and there
is another charged aspartic acid residue in the vicinity, other than that
I'm not sure of what other features may be significant.

Thank you very much for your time and I am also sorry for the trouble.

Regards,

Ming Hui

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