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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 25 2011 - 05:00:03 PDT
