AMBER Archive (2003)

Subject: solventbox at constant pressure

From: Petrodler_at_aol.com
Date: Wed Jun 04 2003 - 02:19:05 CDT

Dear Amber users,

I have a question about simulating a solvent at constant pressure.
I created a solventbox in xleap with 95 residues by solvating a molecule by itself. The minimization of energy and the equilibration from 0 to 300 K at constant volume of this box in sander was no problem. But when I start the md simulation at constant pressure in sander the simulation aborts after a few steps:

MPI abort by user aborting program

EWALD BOMB in subroutine ewald_list
Volume of ucell too big, too many subcells
List grid memory needs to be reallocated, restart sander

The first step of simulation:

NSTEP = 0 TIME(PS) = 0.001 TEMP(K) = 0.00
PRESS =270717.7
 Etot = 6782.0005 EKtot = 0.0000
EPtot = 6782.0005
BOND = 270.9596 ANGLE = 1599.5166
DIHED = 804.8136
 1-4 NB = 497.8652 1-4 EEL = -5.5765
VDWAALS = 3602.0229
 EELEC = 12.3992 EHBOND = 0.0000
RESTRAINT = 0.0000
 EKCMT = 0.0000 VIRIAL = -60964.2405
VOLUME =10429.9122
Density = 1.2729

The step before the simulation aborts:

NSTEP = 1800 TIME(PS) = 0.037 TEMP(K) = 127.55
PRESS = 15560.4
 Etot = 1476.7078 EKtot = 505.2900
EPtot = 971.4179
 BOND = 64.0907 ANGLE = 562.1510
DIHED = 639.1385
 1-4 NB = 260.3182 1-4 EEL = -5.7039
VDWAALS = -560.8595
 EELEC = 12.2829 EHBOND = 0.0000
RESTRAINT = 0.0000
 EKCMT = 28.3271 VIRIAL = -5107.0993
VOLUME = 185.4596
Density = 0.8685

I want to simulate three different solvents, but for every solvent I had the same problem.
I changed the parameters for the simulation several times and a tried the simulation with a larger and a smaller solventbox, but it was always the same problem.

My input-file:

&cntrl
   ntpr=50, ntwx=100, ntwr=500, iwrap=1, cut=6.0,
   ntf=2, ntc=2, tol=0.000001, ntb=2,
   nstlim=2000, dt=0.00002, nscm=1000,
   tempi=0.0, temp0=300.0, ntt=1, tautp=1.0,
   pres0=1.0, taup=0.2,
   ntp=1,
 &end

-----------------------------------------------------------------------------
   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 = 50, ntrx = 1, ntwr = 500
     iwrap = 1, ntwx = 100, 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
     dielc = 1.00000, cut = 6.00000,
intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
     ibelly = 0, ntr = 0
Molecular dynamics:
     nstlim = 2000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00002,
     vlimit = 20.00000
Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 300.00000, tempi = 0.00000,
     heat = 0.00000
     dtemp = 5.00000, tautp = 1.00000
Pressure regulation:
     ntp = 1, plevel = 1
     pres0 = 1.00000, comp = 44.60000,
     taup = 0.20000
SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00000
Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
     Box X = 21.646 Box Y = 22.518 Box Z = 21.398
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 24 NFFT2 = 24 NFFT3 = 24
     Cutoff= 6.000 Tol =0.100E-04
     Ewald Coefficient = 0.47291
     Interpolation order = 4

What`s the problem with this simulation ? Is there any problem by creating the solventbox in xleap ?
Thanks in advance.

Peter Trodler
Institute for Technical Biochemistry
University of Stuttgart