- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Sangita Kachhap <sangita.imtech.res.in>

Date: Mon, 21 Jun 2010 16:40:28 +0530 (IST)

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jun 21 2010 - 04:30:07 PDT

Date: Mon, 21 Jun 2010 16:40:28 +0530 (IST)

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Jun 21 2010 - 04:30:07 PDT

Custom Search