Hello!
Im trying to run a system that is a octamer with more than 88000 molecules and my simulations crush on the 1st equilibration step, just after minimization.
1. How was wondering if the sequence to list the molecules affects the way that amber reads the structure, I mean, in my structure the numbers after 9999 are written from left to right :
ATOM 68851 O WAT 9999 70.257 33.414 43.443 1.00 0.00
ATOM 68852 H1 WAT 9999 69.819 32.698 42.984 1.00 0.00
ATOM 68853 H2 WAT 9999 70.998 33.642 42.881 1.00 0.00
TER
ATOM 68854 O WAT 10000 67.047 28.104 49.964 1.00 0.00
ATOM 68855 H1 WAT 10000 66.234 28.403 50.371 1.00 0.00
ATOM 68856 H2 WAT 10000 67.543 27.709 50.682 1.00 0.00
instead of the traditional count from right to left:
ATOM 68851 O WAT 9999 70.257 33.414 43.443 1.00 0.00
ATOM 68852 H1 WAT 9999 69.819 32.698 42.984 1.00 0.00
ATOM 68853 H2 WAT 9999 70.998 33.642 42.881 1.00 0.00
TER
ATOM 68854 O WAT 10000 67.047 28.104 49.964 1.00 0.00
ATOM 68855 H1 WAT 10000 66.234 28.403 50.371 1.00 0.00
ATOM 68856 H2 WAT 10000 67.543 27.709 50.682 1.00 0.00
2. I donīt see any clashes but my output says:
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
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
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.39
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.84
|---------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 144.03 PRESS = 0.0
Etot = ************** EKtot = 90427.4736 EPtot = **************
BOND = 2350.9848 ANGLE = 9329.9526 DIHED = 33698.7221
1-4 NB = 17712.5851 1-4 EEL = 128806.2210 VDWAALS = **************
EELEC = -1078125.2640 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.7221E-03
------------------------------------------------------------------------------
Any suggestions on how to change my input file to overcome this issue?
Input:
# Start MD from coordinates. Assign velocities for tempi=100K and warm up to 150K
# Set "restraintmask" & "restraint_wt" to the correct values for your system
#
&cntrl
timlim=999999., imin=0,
ntx=1,
ntxo=1, ntpr=1000, ntwx=1000, ntwv=0, ntwe=1000, ioutfm=1,
ntp=0, ntc=2,
ntb=1, ntf=2, cut=9.0,
ntt=3, temp0=150, tempi=100, ig=-1, gamma_ln=2.0,
nstlim= 1000000, dt=0.002,
iwrap=1, nrespa=1,
/
~
Thank you,
Ana
************************************************
Ana Oliveira, PhD
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-751 24 Uppsala
Sweden
email: analuisa.novodeoliveira.icm.uu.se
Webpage: http://www.icm.uu.se/research/csb/aqvist/
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Received on Fri Sep 22 2017 - 05:00:01 PDT
