AMBER Archive (2003)

Subject: vlimit exceeded when sander calculate free energies using TI

From: zsx (zsx163_at_163.com)
Date: Wed Jun 11 2003 - 06:51:09 CDT


Dear amber,
 I have used the Cap water , ibelly=1 and ntb=0, it can run normally dynamics in sander7, but when I use the normal dynamic *.rst as the input file for sander7 TI calculation, icfe=1 and clambda=0.04691, the VDW energy and Temperature will increase uncontrolly, then break down. I want to know the reason, for it seem that it will go normally with period condition system.

the normal dynamics input file:
&cntrl
irest=0,ibelly=1,
ntx=1, tempi=310.0, temp0=310.0,
ntb=0, ntp=0,
ntt=1, tautp=0.2,
dtemp=2.0,
nstlim=10000, dt=0.001,
 ntc=2, ntf=2,
 scee=1.2,
cut=12,nsnb=20,
ntpr=100, ntwx=0,
vlimit=20.0,
&end
--CUTRES
RES 1 1
..
END
END
the TI input file:
&cntrl
 irest=0,ibelly=1,
ntx=1, tempi=310.0, temp0=310.0,
ntb=0, ntp=0,
ntt=1, tautp=0.2,
dtemp=2.0,
nstlim=10000, dt=0.001,
  ntc=2, ntf=2,
 scee=1.2,
cut=12,nsnb=20,
ntpr=100, ntwx=0,
vlimit=20.0,
 icfe=1,clambda=0.04691, ntave=2000,
&end
--CUTRES
RES 1 1
..
END
END

the output file with error:
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 0, igb = 0, nsnb = 20
     ipol = 0, gbsa = 0
     dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 1, ntr = 0

Molecular dynamics:
     nstlim = 10000, nscm = 9999999, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 310.00000, tempi = 310.00000, heat = 0.00000
     dtemp = 2.00000, tautp = 0.20000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

Free energy options:
     klambda = 1
     clambda = 0.04691

Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!

| PLEVEL = 1: runmd parallelization, no EKCMR

    LOADING THE BELLY ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 --CUTRES c1 1194:
 GRP 1 RES 1 TO 1
 GRP 1 RES 61 TO 61
 GRP 1 RES 63 TO 86
 GRP 1 RES 88 TO 88
 GRP 1 RES 92 TO 92
 GRP 1 RES 96 TO 96
 GRP 1 RES 98 TO 98
 GRP 1 RES 110 TO 130
 GRP 1 RES 133 TO 133
 GRP 1 RES 141 TO 153
 GRP 1 RES 167 TO 168
 GRP 1 RES 171 TO 171
 GRP 1 RES 194 TO 207
 GRP 1 RES 221 TO 227
 GRP 1 RES 229 TO 234
 GRP 1 RES 238 TO 238
 GRP 1 RES 241 TO 242
 GRP 1 RES 245 TO 246
 GRP 1 RES 249 TO 250
 GRP 1 RES 269 TO 292
 GRP 1 RES 318 TO 341
 GRP 1 RES 343 TO 343
 GRP 1 RES 345 TO 345
 GRP 1 RES 349 TO 349
 GRP 1 RES 352 TO 360
 GRP 1 RES 386 TO 386
 GRP 1 RES 389 TO 399
 GRP 1 RES 401 TO 402
 GRP 1 RES 419 TO 425
 GRP 1 RES 427 TO 449
 GRP 1 RES 456 TO 456
 GRP 1 RES 467 TO 467
 GRP 1 RES 471 TO 471
 GRP 1 RES 471 TO 471
 GRP 1 RES 503 TO 503
 GRP 1 RES 535 TO 536
 GRP 1 RES 538 TO 1233
      Number of atoms in this group = 5415
    ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords = 100.000 ps

| Reorder water Setup:
| Reorder water will be done on atoms : 8414 10501
|
 Number of triangulated 3-point waters found: 696
| Atom division among processors:
| 0 5255 10501
| Running AMBER/MPI version on 2 nodes

     Sum of charges from parm topology file = 0.00299979
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=5: Using 1/r dielectric

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1572433
| TOTAL SIZE OF NONBOND LIST = 3142890
 vlimit exceeded for step 0 ; vmax = 7766.6054701455487
 vlimit exceeded for step 1 ; vmax = 72981734.699283138
 vlimit exceeded for step 2 ; vmax = 1372304881.9659796
 vlimit exceeded for step 3 ; vmax = 3753.7947883563297
 vlimit exceeded for step 4 ; vmax = 80.475719565907056
 vlimit exceeded for step 5 ; vmax = 527.63477952372773
 vlimit exceeded for step 6 ; vmax = 2197.5585529658647
 vlimit exceeded for step 7 ; vmax = 184.4416200076885
 vlimit exceeded for step 8 ; vmax = 277.33377692621201

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 4 137 1299 1297

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

Thank you
sxzheng