I have been working with "cubes" of water, but I wanted to try a TO. I
have a small 20 residue peptide structure that I've placed in a TO using
the procedure in the Amber6 tutorial (leap gives a cube using WATBOX216,
ptraj chops it into a TO using "truncoct :1-20 10.0 prmtop oct_top.prm")
I then minimized the water while fixing residues 1-20 and then minimized
the entire system. I then started a 10ps MD run in which residues 1-20
were again fixed. Looking at the resulting structure (I used iwrap=1), I
noticed my peptide is very close to one edge of the TO, leading to my
first question:
1) Does it matter if my solute of interest appears to get near an edge of
the TO using iwrap=1, or does this make no difference from a simulation
point of view.
My bigger problem is that if I take the coordinate file (restrt) from that
run and then try to apply it to a long runner with no fixed residues,
sander immediately crashes with:
NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 727.10 PRESS =**********
Etot = ************ EKtot = 9000.9543 EPtot = ************
BOND = 104.0038 ANGLE = 242.8940 DIHED = 144.2317
1-4 NB = 76.9501 1-4 EEL = 871.9589 VDWAALS = ************
EELEC = -11424.0419 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 2817.9106 VIRIAL = ************ VOLUME = 85720.1675
Density = 0.7229
Ewald error estimate: 0.1067E-03
------------------------------------------------------------------------------
COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
DEVIATION IS TOO LARGE
NITER, NIT, LL, I AND J ARE : 0 0 42 83 84
This doesn't make sense to me, as the final mdinfo written in the first md
run ans the starred values within ok ranges:
NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 493.15 PRESS = -237.87
Etot = -7754.5543 EKtot = 6104.7889 EPtot = -13859.3431
BOND = 97.1805 ANGLE = 228.5314 DIHED = 149.7346
1-4 NB = 73.3083 1-4 EEL = 855.4814 VDWAALS = 1369.0613
EELEC = -16632.6405 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 2827.3824 VIRIAL = 3275.7318 VOLUME = 87296.2099
Density = 0.7099
Ewald error estimate: 0.3716E-03
So question two:
2) Why can't I get an MD run to start in Sander using the restrt file from
my previous run? (I've never had this type of problem with cubes)
Thanks for your help. I've included my second MD run file below.
Robert
&cntrl
imin=0,
irest=0,
ntpr=100,
ntwr=100,
ntwx=1000,
ntwe=100,
ntf=2,
ntb=2,
nstlim=50000,
dt=.001,
temp0=498,
tempi=498,
ntt=1,
tautp=1.0,
ntp=1,
taup=1.0,
ntc=2,
iwrap=1,
&end
_________________________
R. M. Fesinmeyer
rmf_at_u.washington.edu
Department of Chemistry
University of Washington
Received on Thu Nov 16 2000 - 15:44:31 PST
