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
Received on Wed Jun 11 2003 - 13:53:01 PDT
