AMBER: problem at the start of heating up (using extra-point)

From: Rachel <comeonsos.googlemail.com>
Date: Sat, 2 Dec 2006 15:29:09 +0000

Dear all,

I have a problem after minimization when I tried to heat up my system, this
is my how I did the heating up:
#######################################################
MD with res on the protein
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 20000, dt = 0.0005,
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
Keep protein fixed with weak restraints
10.0
RES 1 791
END
END
#############################################################

When I use dt > 0.5fs (I tried dt=0.001, 0.0009, 0.0008, 0.0007, 0.0006), I
got the error message like this:
##############################################################

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 Etot = -218706.4292 EKtot = 0.0000 EPtot = -
218706.4292
 BOND = 402.6962 ANGLE = 2165.9364 DIHED =
6766.3301
 1-4 NB = 2505.1240 1-4 EEL = 34266.4936 VDWAALS =
26154.1679
 EELEC = -290967.1774 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.8028E-04
 ------------------------------------------------------------------------------

 vlimit exceeded for step 0 ; vmax = Infinity

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 65751215812159

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

######################################################################

The I and J are different when I used different timestep.

As I kept decrease the timestep to 0.5fs, I got different error message:
######################################################################

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 Etot = -218706.4292 EKtot = 0.0000 EPtot = -
218706.4292
 BOND = 402.6962 ANGLE = 2165.9364 DIHED =
6766.3301
 1-4 NB = 2505.1240 1-4 EEL = 34266.4936 VDWAALS =
26154.1679
 EELEC = -290967.1774 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.8028E-04
 ------------------------------------------------------------------------------

 vlimit exceeded for step 0 ; vmax = Infinity

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
#########################################################################

And if I kept decrease the timestep, I got the same message as above.

Also I have tried to change temp0 to smaller value (like 50), still I had
the same problem.
I am not whether this is relevant, I have treated some of my atoms (hydrogen
atoms) as extra-points as suggested by David Case, and I have such lines in
my MD output:
###########################################################################

   5. REFERENCE ATOM COORDINATES


    ----- READING GROUP 1; TITLE:
 Keep protein fixed with weak restraints

     GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
 GRP 1 RES 1 TO 791
      Number of atoms in this group = 12156
    ----- END OF GROUP READ -----
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 49969 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 49969 0
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 6328 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 6328 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 13725 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 13725 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 8660 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 8660 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 25765 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 25765 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 16154 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 16154 0

########################################################################

Does anyone know how to solve this problem? any suggestion is so much
appreciated. Thank you in advance.

Best regards,

Rachel

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Received on Sun Dec 03 2006 - 06:08:08 PST
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