AMBER Archive (2006)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sat Dec 02 2006 - 11:32:50 CST


Hi,

I think seeing your input for minimization could also be helpful.
Take a look at your trajectory if bubbles form during the heat-up process.
How did you solvate your system?
Try the following solvation process in leap:
"solvateoct mol TIP3PBOX 10 0.4"
see if that improves your minimization and warm-up processes..
Also, looking at your input that you sent, here are a few comments:
try using the following parameters in your input :
 dt=0.002,
  cut=9,
  gamma_ln=10,
  vlimit=5,

hope that helps,

regards,

jenk

 

Rachel <comeonsos_at_googlemail.com> wrote: 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

  
 

         
---------------------------------
Everyone is raving about the all-new Yahoo! Mail beta.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu