Hi, I know this is sort of a used up question in the archive but i cannot
find anyone having the same problem as this.
I minimized my structure holding ligand rigid for many cycles (6000 maxcyc)
and warmed the system (system = protein/ligand/water) to 300K for 20 ps. I
think it went fine, here is the input and last output of that run,
polyA-polyT 10-mer: 20ps MD with res on DNA
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep PMK fixed with weak restraints
20.0
RES 1 189
END
END
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 300.34 PRESS =
0.0
Etot = -58624.3726 EKtot = 15107.1350 EPtot =
-73731.5075
BOND = 576.7693 ANGLE = 1326.1141 DIHED =
1989.0217
1-4 NB = 666.6005 1-4 EEL = 3493.6884 VDWAALS =
7716.6018
EELEC = -90240.1295 EHBOND = 0.0000 RESTRAINT =
739.8263
EAMBER (non-restraint) = -74471.3338
Ewald error estimate: 0.4748E-04
------------------------------------------------------------------------------
A V E R A G E S O V E R 10000 S T E P S
NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 282.99 PRESS =
0.0
Etot = -60813.2526 EKtot = 14234.8192 EPtot =
-75048.0719
BOND = 560.6399 ANGLE = 1275.5163 DIHED =
1965.1125
1-4 NB = 668.5587 1-4 EEL = 3503.3026 VDWAALS =
8281.0984
EELEC = -92021.3667 EHBOND = 0.0000 RESTRAINT =
719.0665
EAMBER (non-restraint) = -75767.1384
Ewald error estimate: 0.6906E-04
------------------------------------------------------------------------------
Well from here i naturally tried to restart it with a production time of 100
ps and here is the input and error i get for it,
protein 20ps MD with res lig
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
pres0 = 1.0,
ntp = 1,
taup = 2.0
cut = 10,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep lig fixed with weak restraints
20.0
RES 189
END
END
---------------------------------------------------
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 = 7723070
| TOTAL SIZE OF NONBOND LIST = 7723070
vlimit exceeded for step 27; vmax = 24.0912
vlimit exceeded for step 28; vmax = 26.7198
vlimit exceeded for step 44; vmax = 31.3538
vlimit exceeded for step 50; vmax = 28.6795
vlimit exceeded for step 66; vmax = 32.6102
vlimit exceeded for step 70; vmax = 27.8292
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 1504 3016 3017
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I understand that something is wrong with my complex but im not sure how to
fix it while keeping my last run good and not re-doing the warming up phase.
Any thoughts? Thanks
Drew
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 17 2009 - 10:10:01 PDT
