Try visualizing your system (both during heating and during MD). Do you see
anything weird happening?
I would strongly suggest that you heat more carefully. Due to the nature of
the constant pH simulations (changing charges periodically), atomic
fluctuations tend to be higher, and systems fall apart more easily during
heating.
You can get around this by heating with restraints. I typically restrain
the backbone atoms (restraintmask='.CA,C,O,N') with a fairly strong
restraint (restraint_wt=2.0 to 5.0), then equilibrate at constant T with a
smaller restraint_wt (0.5 to 1).
Hope this helps,
Jason
On Fri, Mar 25, 2011 at 4:38 AM, pankhuri arora <pankhuri2001.gmail.com>wrote:
> Dear Amber users,
>
> I am running a constant pH simulation on a protein with Amber 11 and I am
> getting the error mentioned below. I did energy minimization twice , first
> for 200cycles with SHAKE on ntc=2 and then for 5000 cycles without SHAKE
> with the following parameters:
>
> # 200 steps of minimization
> &cntrl
> imin=1, ntmin=1, maxcyc=200, ncyc=100,
> cut=30.0, igb=2, saltcon=0.1
> ntx=1, irest=0, ntb=0, ntpr=5
> ntc=2, ntf=2,
> ntwx=10, ntwv=10, ntwe=10, ntwr=10
> /
>
> # 5000 steps of minimization
> &cntrl
> imin=1, ntmin=1, maxcyc=5000, ncyc=2500,
> cut=30.0, igb=2, saltcon=0.1
> ntx=1, irest=0, ntb=0, ntpr=5
> ntc=1, ntf=1,
> ntwx=10, ntwv=10, ntwe=10, ntwr=10
> /
>
> Then I heated the system to 300K using the following parameters:
>
> #Heating from 0K to 300K
> &cntrl
> imin=0,
> irest=0,ntx=1,ntb=0,cut=30.0,
> ntpr=200,ntwx=200,ntwr=500,ntwv=200,ntwe=200
> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> nstlim=150000,dt=.002,
> ntt=1,tempi=0,temp0=300,nmropt=1,
> saltcon=0.1,tol=0.000001
> icnstph=1, ntcnstph=5, solvph=6.0
> /
> &wt TYPE='TEMP0', istep1=0, istep2=150000,
> value1=0.0, value2=300.0, /
> &wt TYPE='END' /
>
> Finally I ran the 1ns simulation and got the following error:
>
> NSTEP = 140000 TIME(PS) = 680.000 TEMP(K) = 300.31 PRESS =
> 0.0
> Etot = -2752.7777 EKtot = 1488.6555 EPtot =
> -4241.4332
> BOND = 401.1401 ANGLE = 1026.9172 DIHED =
> 1369.9518
> 1-4 NB = 418.4399 1-4 EEL = 3814.9936 VDWAALS =
> -915.6806
> EELEC = -8793.8949 EGB = -1563.3004 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
> NSTEP = 140500 TIME(PS) = 681.000 TEMP(K) = 299.18 PRESS =
> 0.0
> Etot = -2748.7606 EKtot = 1483.0493 EPtot =
> -4231.8098
> BOND = 392.6345 ANGLE = 1004.1752 DIHED =
> 1370.9104
> 1-4 NB = 426.6309 1-4 EEL = 3817.8609 VDWAALS =
> -934.6953
> EELEC = -8366.1129 EGB = -1943.2135 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 140543; vmax = 204.0262
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 14 19 21
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> Here is my mdin file :
> #Constant pH in GB on HEWL
> &cntrl
> ig=49,
> nstlim=50000
> cut=30.0, igb=2, saltcon=0.1,
> ntx=5, irest=1, ntb=0,
> dt=0.002, nrespa=1,
> ntt=1, temp0 = 300.0, tautp=2.0,
> ntc=2, ntf=2, tol=0.000001,
> ntwx=500, ntwv=500, ntpr=500, ntwe=500, ntwr=500,
> icnstph=1, ntcnstph=5, solvph=6.0
> /
>
> Any suggestions please? Thanks in advance
>
> Regards,
> Pankhuri
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 25 2011 - 08:30:02 PDT
