Hi! I was hoping someone could advise me regarding a problem I am having
with lambda points in TI calculations. I am using Amber 10 and am following
the protocol listed in tutorial A9. I wanted to put lambda pints at 0.05 and
0.95 (to improve final numerical integration), but I get a vlimit exceeded
error during the equilibration stage.
I have read that this could be due to the timestep, so have decreased it
from 0.002 to 0.001 and turned shake off. However, I still get the error.
Would this be resolved by using a more stringent two step protocol for
equilibration? i.e. equilibrating temperature first, then density. Or are
there any other aspects to this that I am missing. I have enclosed one of
the out files for lambda 0.95 below. Your help would be greatly appreciated.
best regards
GT
##########################################
File Assignments:
| MDIN:
mdin_equi_v0_l95
| MDOUT:
hexanol_ligand_equi_v0_l95.out
|INPCRD:
hexanol_ligand_min_v0_l95.rst
| PARM:
../hexanol_ligand.parm
|RESTRT:
hexanol_ligand_equi_v0_l95.rst
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
hexanol_ligand_equi_v0_l95.crd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
|
Here is the input file:
density
equilibration
&cntrl
imin = 0, ntx = 1, irest = 0, ig =
-1,
ntpr = 250, ntwr = 1000, ntwx =
250,
ntf = 2, ntc =
1,
ntb = 2, cut =
9.0,
nstlim = 25000, dt =
0.001,
temp0 = 278, ntt = 3, gamma_ln =
5,
ntp = 1, pres0 = 1.0, taup =
0.2,
icfe=1, clambda =
0.95,
ifsc=0,
crgmask='',
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 13.908
| New format PARM file being parsed.
| Version = 1.000 Date = 11/12/09 Time = 15:44:40
NATOM = 1701 NTYPES = 7 NBONH = 1694 MBONA = 6
NTHETH = 32 MTHETA = 5 NPHIH = 45 MPHIA = 10
NHPARM = 0 NPARM = 0 NNB = 2346 NRES = 561
NBONA = 6 NTHETA = 5 NPHIA = 10 NUMBND = 7
NUMANG = 8 NPTRA = 8 NATYP = 7 NPHB = 1
IFBOX = 1 NMXRS = 21 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 170577
| Hollerith 10769
| Integer 58112
| Max Pairs 377338
| nblistReal 20412
| nblist Int 72790
| Total 3519 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 250, ntrx = 1, ntwr =
1000
iwrap = 0, ntwx = 250, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 25000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 461100
temp0 = 278.00000, tempi = 0.00000, gamma_ln= 5.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 0.20000
Free energy options:
icfe = 1, ifsc = 0
klambda = 1
clambda = 0.95000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 34.987 Box Y = 28.371 Box Z = 27.817
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 36 NFFT2 = 30 NFFT3 = 27
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 560
| Atom division among processors:
| 0 852 1701
Sum of charges from parm topology file = -0.00030000
Forcing neutrality...
| Running AMBER/MPI version on 2 nodes
| MULTISANDER: 2 groups. 2 processors out of 4 total.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 5103.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 5103. NUM_NOSHAKE = 0 CORRECTED RNDFP = 5103.
| TOTAL # of degrees of freedom (RNDF) = 5103.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 132744
| TOTAL SIZE OF NONBOND LIST = 311326
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-2229.2
Etot = -6850.4325 EKtot = 0.0000 EPtot =
-6850.4325
BOND = 0.1242 ANGLE = 0.9550 DIHED =
2.3894
1-4 NB = 1.4486 1-4 EEL = 0.0095 VDWAALS =
1397.4789
EELEC = -8252.8382 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 0.0363
EKCMT = 0.0000 VIRIAL = 1328.9095 VOLUME =
27610.5022
Density =
0.6129
Ewald error estimate: 0.2706E-03
------------------------------------------------------------------------------
vlimit exceeded for step 11; vmax = 488.1186
vlimit exceeded for step 12; vmax = 348.7365
vlimit exceeded for step 13; vmax = 476.1181
vlimit exceeded for step 14; vmax = 1107.8662
vlimit exceeded for step 15; vmax = 1210.8087
vlimit exceeded for step 16; vmax = 1076.5600
vlimit exceeded for step 17; vmax = 486.9208
vlimit exceeded for step 18; vmax = 183.4240
vlimit exceeded for step 19; vmax = 318.7466
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
################################################################
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Received on Mon Aug 16 2010 - 12:00:05 PDT
