[AMBER] Error: vlimit exceeded for step

From: pankhuri arora <pankhuri2001.gmail.com>
Date: Fri, 25 Mar 2011 16:38:11 +0500

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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Received on Fri Mar 25 2011 - 05:00:03 PDT
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