Hi
I am Aparna.P from M.G.University,Kerala,India.
I am working on MD on Biomolecules.
I got a problem while I was doing simulation of a system.
My system has 12561 atoms including water molecules.
My input is
i min =0,
irest =0,
ntx =1,
ntb =1,
cut =10,
ntr =1,
ntc =2,
ntf =2,
tempi =0.0,
temp0=150.0,
ntt =3,
gamma_ln=1,
nstlim =25000, dt =0.002,
ntpr=500,ntwx=500,ntwr =1000,
nmropt =1,
/
&wt type='TEMPO' , istep =0,istep2 =25000,value1=0.0,value2=150.0,
/
&wt type = 'END'
/
restraints
10.0
RES 1 20
END
END
I attach the energies of the system in MD script
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -60915.8860 EKtot = 0.0000 EPtot =
-60915.8860
BOND = 46.0249 ANGLE = 545.6061 DIHED =
535.0389
1-4 NB = 259.1070 1-4 EEL = -5583.3665 VDWAALS =
10203.6931
EELEC = -66921.9894 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2769E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 58.22 PRESS =
0.0
Etot = -51315.5240 EKtot = 1479.8931 EPtot =
-52795.4171
BOND = 75.7294 ANGLE = 599.8928 DIHED =
552.7123
1-4 NB = 272.6463 1-4 EEL = -5596.9545 VDWAALS =
8170.3153
EELEC = -56901.3723 EHBOND = 0.0000 RESTRAINT =
31.6135
EAMBER (non-restraint) = -52827.0306
Ewald error estimate: 0.8510E-04
-----------------------------------------------------------------------
=======
vlimit exceeded for step 10315; vmax = 256.3785
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 4 21 22
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
i dont know why it happened.Can anyone tell me why it happened.
Regards
Aparna.P
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Received on Mon Sep 12 2011 - 00:00:03 PDT
