Hello all
I am doing constant ph simulation ,I did the folowing steps:
1)minimization
Minimized the system using folowing input file:
imin=1, igb=2,
maxcyc=1000, ncyc=300,
ntr=1, cut=30, ntb=0
restraint_wt=30.0,restraintmask='.CA,N,C,O'
2)Heat the system for 300ps using folowing input file:
imin=0,
irest=0,ntx=1,ntb=0,cut=30,
ntpr=100,ntwx=100,ntwr=500,
igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
nstlim=150000,dt=.002,ntr=1,
ntt=1,tempi=0,temp0=300,nmropt=1,
scee=1.2,saltcon=0.1,tol=0.000001,
restraint_wt=2.0,restraintmask='.CA,N,C,O'
icnstph=1,solvph=4,ntcnstph=5
&end
&wt
type='TEMP0', istep1=0, istep2=10000, value1=0, value2=20,
&end
&wt
type='TEMP0', istep1=10001, istep2=20000, value1=20, value2=40,
&end
&wt
When I used the restraint_wt=5.0 it stoped after 299ps
NSTEP = 149500 TIME(PS) = 299.000 TEMP(K) = 291.57 PRESS = 0.0
Etot = -2691.9053 EKtot = 1449.9721 EPtot = -4141.8773
BOND = 370.2844 ANGLE = 972.8162 DIHED = 1361.3202
1-4 NB = 463.3007 1-4 EEL = 3832.7439 VDWAALS = -1014.4626
EELEC = -8382.9596 EGB = -1862.4313 RESTRAINT = 117.5108
EAMBER (non-restraint) = -4259.3882
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 149503; vmax = 359.2528
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 2 19 21
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
3)equilibration for 100ps
imin=0,
irest=1,ntx=7,ntb=0,cut=30,
ntpr=200,ntwx=200,ntwr=500,
igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
nstlim=50000,dt=.002,ntr=1,
ntt=1,tempi=300,temp0=300,
scee=1.2,saltcon=0.1,tol=0.000001,
icnstph=1,solvph=4,ntcnstph=5
restraintmask='.CA,N,C,O',restraint_wt=0.5
/
When Iused the restraint_wt=1.5 again I got the same problem
4)production
irest=1,ntx=7,ntb=0,cut=30,
ntpr=200,ntwx=200,ntwr=500,
igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
nstlim=250000,dt=.002,
ntt=1,tempi=300,temp0=300,
scee=1.2,saltcon=0.1,tol=0.000001,
icnstph=1,solvph=4,ntcnstph=5
/
It stoped after 820ps
NSTEP = 210400 TIME(PS) = 820.800 TEMP(K) = 297.92 PRESS = 0.0
Etot = -2646.0126 EKtot = 1481.5587 EPtot = -4127.5713
BOND = 389.7766 ANGLE = 1026.9842 DIHED = 1360.8354
1-4 NB = 431.5990 1-4 EEL = 3907.9110 VDWAALS = -869.7890
EELEC = -8263.1458 EGB = -2111.7427 RESTRAINT = 0.0000
------------------------------------------------------------------------------
vlimit exceeded for step 210546; vmax = 62.4792
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 2 19 21
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
What is the problem i am not geting why my sytem blows up.
One more thing what is the distance criteria for two close carboxylates so that
there is requirement of modification in cpin file?
Can anybody suggest me what I should do.
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Jun 22 2010 - 13:00:03 PDT
