AMBER Archive (2004)

Subject: AMBER: sander + vlimit exceed...

From: Carsten Detering (detering_at_u.washington.edu)
Date: Thu Feb 26 2004 - 17:16:31 CST

Dear Ambers,

I am calculating a protein-ligand complex, following a paper by David
Case (Biopolymers, 2003). In order to prepare for gibbs, I minimized the
solvent molecules (water) beforehand for 10000 steps (infact, the
COMPLEX was minimized in MOE using the Amber FF before I loaded it into
Amber). This was the input file for the minimization:

&cntrl
imin=1, maxcyc = 10000, ncyc = 10, ntmin = 0
ntpr = 5
ntr = 1
ntb = 1
&end

50.0
RES 1 290
END
END

Then I am running an MD calculation, still with restraints on the solute
atoms. I used 25.0 as a value before (like in the paper), but I got a
warning that the "vlimit exceeded for step". One hint in the mail
reflector was to reduce the restraints to less than 15.0. And to not
calculate the system directly at 300.0 K. So I use a restraint vlaue of
10.0 and gradually heated up the system from 0.0 to 300.0 K. But this
didn't help either. i still have vlimit exceeded warnings, plus, the
temperature is incredibly high, although I set the temp0 to 300.0. can
anyone tell me why that is?

Here is the input file for the MD run:

&cntrl

imin = 0

irest = 0

nstlim = 3500

dt = 0.001

ntx = 1

ntt =1, tempi = 0.0, temp0 = 300.

ntr = 1

ntb = 1

ntpr = 1

ntwx = 1

&end

 

10.0

RES 1 290

END

END

And this is part of the output:

vlimit exceeded for step 2234; vmax = 7933.80843

  NSTEP = 2235 TIME(PS) = 2.235 TEMP(K) =460408.72 PRESS = 0.0
  Etot = ************ EKtot = ************ EPtot = 1387047.7148
  BOND = 712888.1536 ANGLE = 173285.8883 DIHED = 13731.2831
  1-4 NB = 148394.8399 1-4 EEL = 7635.2987 VDWAALS = 190936.7419
  EELEC = -150792.7008 EHBOND = 0.0000 RESTRAINT = 290968.2102
  EAMBER (non-restraint) = 1096079.5046
  Ewald error estimate: 0.5468E-04
 
------------------------------------------------------------------------------

  vlimit exceeded for step 2235; vmax = 114048652.

  NSTEP = 2236 TIME(PS) = 2.236 TEMP(K) =********* PRESS = 0.0
  Etot = ************ EKtot = ************ EPtot = ************
  BOND = 712455.7699 ANGLE = 175321.4375 DIHED = 13509.1954
  1-4 NB = ************ 1-4 EEL = 7682.5213 VDWAALS = 109145.5181
  EELEC = -150627.9297 EHBOND = 0.0000 RESTRAINT = 292305.1309
  EAMBER (non-restraint) = ************
  Ewald error estimate: 0.4943E-04
 
------------------------------------------------------------------------------

  vlimit exceeded for step 2236; vmax = 119165.668

  NSTEP = 2237 TIME(PS) = 2.237 TEMP(K) =********* PRESS = 0.0
  Etot = ************ EKtot = ************ EPtot = 1715452.0721
  BOND = 720124.3962 ANGLE = 176114.5066 DIHED = 13561.0712
  1-4 NB = 477432.9920 1-4 EEL = 7651.3494 VDWAALS = 177759.0851
  EELEC = -150470.5397 EHBOND = 0.0000 RESTRAINT = 293279.2114
  EAMBER (non-restraint) = 1422172.8607
  Ewald error estimate: 0.2285E-04
 
------------------------------------------------------------------------------

  vlimit exceeded for step 2237; vmax = 828779.934

  NSTEP = 2238 TIME(PS) = 2.238 TEMP(K) =********* PRESS = 0.0
  Etot = ************ EKtot = ************ EPtot = 5461102.9215
  BOND = 731757.4434 ANGLE = 176550.6847 DIHED = 13902.5372
  1-4 NB = 1789909.4686 1-4 EEL = 7395.7559 VDWAALS = 2598854.5787
  EELEC = -150428.1583 EHBOND = 0.0000 RESTRAINT = 293160.6112
  EAMBER (non-restraint) = 5167942.3102
  Ewald error estimate: 0.2639E-04
 
------------------------------------------------------------------------------

  vlimit exceeded for step 2238; vmax = 69061.3301

  NSTEP = 2239 TIME(PS) = 2.239 TEMP(K) =********* PRESS = 0.0
  Etot = ************ EKtot = ************ EPtot = 1503651.3111
  BOND = 737433.0876 ANGLE = 178937.3613 DIHED = 13857.8790
  1-4 NB = 161733.2633 1-4 EEL = 7134.3063 VDWAALS = 262245.4705
  EELEC = -150393.5742 EHBOND = 0.0000 RESTRAINT = 292703.5174
  EAMBER (non-restraint) = 1210947.7937
  Ewald error estimate: 0.1411E-04

Thanks in advance,

Carsten 

-- 

Carsten Detering
University of Washington
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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