Hello all
I am doing constant pH simulation using Amber10.
For this
1) I have minimize protein:
a)using restraint on backbone with force constant 500.0
b)whole sytem with restraint
2)Heating of system for 300ps with temperature increment 1K/1ps,during heating
here i have used tol=.00001 though in manual for constant pH simulation it
is tol=.000001. Actualy I have done it by mistake.Here I restraint backbone with
foce constant 10.0 .
Here is my input file:
imin=0,
irest=0,ntx=1,ntb=0,cut=30,
ntpr=200,ntwx=200,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=0.00001,vlimit=15,
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 ...........
type='END'
/
Hold only backbone atom fixed
10.0
FIND
* * M *
SEARCH
RES 1 129
END
END
3)Equilibration for 300ps using restraint on backbone with force constant 1.0
this time I use tol=.000001 then I got following error:
vlimit exceeded for step 78066; vmax = 321.8661
vlimit exceeded for step 78067; vmax = 24.5430
vlimit exceeded for step 78082; vmax = 399.2392
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 5 2 19 21
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
But when I chage it to tol=.00001 it run upto 300ps
4)In production run again I have use tol=.00001 it stop with following error :
vlimit exceeded for step 262668; vmax = 111.4422
vlimit exceeded for step 262669; vmax = 25.1137
vlimit exceeded for step 262699; vmax = 1960.5580
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.
Here is the input file:
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=150000,dt=.002,
ntt=1,tempi=300,temp0=300,
scee=1.2,saltcon=0.1,tol=0.00001,vlimit=15,
icnstph=1,solvph=4,ntcnstph=5
/
Where is the problem I am not getting so can anybody suggest me
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Jun 21 2010 - 04:30:07 PDT
