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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Received on Mon Jul 20 2009 - 10:08:36 PDT
