AMBER Archive (2009)

Subject: [AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA

From: Sushil Mishra (sushilbioinfo_at_gmail.com)
Date: Mon Jul 20 2009 - 05:40:51 CDT

Hello all
  i am running MM-MBSA of lectin saccharide complex. I did salvation of the
lectin saccharide complex by *solvateoct model2 TIP3PBOX 8.0*. During
the Equilibration
of the solvated complex. I equilibrated the solvated lectin saccharide
complex by carrying out a short minimisation, 50ps of heating and 50 ps of
density equilibration with weak restraints on the complex followed by 1ns of
constant pressure equilibration at 300K. All simulations are at 2 fs time
step and langevin dynamics for temperature control. The input files
equilibtion is as fallows :

RSL complex
 &cntrl
  imin=0,irest=1,ntx=5,
  nstlim=500000,dt=0.002,
  ntc=2,ntf=2,
  cut=8.0, ntb=2, ntp=1, taup=2.0,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  temp0=300.0,
 /

After 183,000 ps its started giving fallowing errors.............

 NSTEP = 183000 TIME(PS) = 506.000 TEMP(K) = 301.18 PRESS =
-43.4
 Etot = -59827.4577 EKtot = 15975.9480 EPtot =
-75803.4057
 BOND = 747.7617 ANGLE = 1849.8541 DIHED =
1284.0211
 1-4 NB = 882.1108 1-4 EEL = 11489.9212 VDWAALS =
7654.0656
 EELEC = -99711.1403 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 6612.6064 VIRIAL = 6851.7902 VOLUME =
255043.0719
                                                    Density =
1.0380
 Ewald error estimate: 0.1124E-03
 ------------------------------------------------------------------------------

 NSTEP = 184000 TIME(PS) = 508.000 TEMP(K) = 297.43 PRESS =
64.1
 Etot = -60049.0588 EKtot tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated

 NSTEP = 326000 TIME(PS) = 792.000 TEMP(K) = 297.76 PRESS =
-275.6
 Etot = -59819.9642 EKtot = 15794.6675 EPtot =
-75614.6317
 BOND = 763.4583 ANGLE = 1878.5382 DIHED =
1274.1277
 1-4 NB = 891.9103 1-4 EEL = 11547.0198 VDWAALS =
7618.3681
 EELEC = -99588.0542 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 6462.2029 VIRIAL = 7977.4735 VOLUME =
254635.3884
                                                    Density =
1.0397
 Ewald error estimate: 0.1596E-04
 ------------------------------------------------------------------------------
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated
tail: equil.out: file truncated

Then again it starts running calculation properly as shown in last. Pase
could anybody suggest me..... what may be problem??? and how can i overcome
from this ? its urgent plz suggest me solutin of this.
Thanking you in advance..

Sincerely
sushil k mishra
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