Hello all
i am running MM-MBSA of lectin saccharide complex. I am solvation complex by
solvateoct model2 TIP3PBOX 8.0. During the *Equilibration of of the
solvated complex*. i am performing the solvated complex by carrying out a
short minimisation, 50ps of heating and 200 ps of density equilibration with
weak restraints on the complex followed by 200ps of constant pressure
equilibration at 300K. All simulations will be run with shake on hydrogen
atoms, a 2 fs time step and langevin dynamics for temperature control. The
input files for equlibration run was as fallows :
heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,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 38,000 steps i am getting fallowing error.............
Ewald error estimate: 0.6852E-04
------------------------------------------------------------------------------
NSTEP = 38000 TIME(PS) = 216.000 TEMP(K) = 299.09 PRESS =
-65.0
Etot = -59739.6710 EKtot = 15865.0296 EPtot =
-75604.7006
BOND = 759.2950 ANGLE = 1898.9389 DIHED =
1258.6049
1-4 NB = 907.8484 1-4 EEL = 11409.1386 VDWAALS =
7652.1440
EELEC = -99490.6704 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 6535.1966 VIRIAL = 6892.5468 VOLUME =
254706.5266
Density =
1.0394
Ewald error estimate: 0.2886E-04
------------------------------------------------------------------------------
NSTEP = 39000 TIME(PS) = 218.000 TEMP(K) = 297.77 PRESS =
-146.2
Etot = -59866.1098 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
.
.
.
.
Please could anybody suggest me. wat may be problem and how can i
overcome from this ?
Thanking you in advance..
--
Sushil K Mishra
Computational Chemistry Laboratory
National Centre for Biomolecular Research
ILBIT, Building A4 - 2.12
Kamenice 5
625 00 Brno
CZECH REPUBLIC
Tel. +420 549 492 521
Mob. +420 774 816 044
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Received on Mon Jul 20 2009 - 10:07:10 PDT
