Hi All,
I am tying to heat my system (protein + bound cofactor) slowly. I am using
ntt =3 with gamma_ln = 1.0, Below mentioned is the script which I am using.
Heating the system linearly with weak restraints
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 12,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
ig = 20933
gamma_ln = 1.0, nmropt=1,
nstlim = 50000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
&wt TYPE='TEMP0', istep1=0, istep2=40000,
value1=0.1, value2=300.0, /
&wt TYPE='DUMPFREQ',ISTEP1=10, /
&wt TYPE='END' /
Keep protein fixed
5.0
RES 1 339
END
END
The equilibration runs fine upto 9100 steps. After that there is* no change
in the mdout file* but the sander job is running. Previously I didnt
included Ig value in my script so I thought that it may be due to Ig value
as I am using ntt=3. Next time I added the Ig value (a random number) but
this time also the run is upto 7100 steps after that there is no change in
the mdout file.
Below mentioned is the last line of my output file:
NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 49.27 PRESS =
0.0
Etot = -211822.1441 EKtot = 5837.1249 EPtot =
-217659.2690
BOND = 323.1122 ANGLE = 956.0308 DIHED =
3200.9235
1-4 NB = 1056.0283 1-4 EEL = 14174.4148 VDWAALS =
35009.8809
EELEC = -272523.6263 EHBOND = 0.0000 RESTRAINT =
143.9667
EAMBER (non-restraint) = -217803.2357
Ewald error estimate: 0.3030E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 7100 TIME(PS) = 14.200 TEMP(K) = 50.36 PRESS =
0.0
Etot = -211664.7202 EKtot = 5966.1111 EPtot =
-217630.8314
BOND = 312.2514 ANGLE = 957.5403 DIHED =
3192.0819
1-4 NB = 1062.4902 1-4 EEL = 14166.2999 VDWAALS =
34826.4805
EELEC = -272299.1537 EHBOND = 0.0000 RESTRAINT =
151.1782
EAMBER (non-restraint) = -217782.0095
Ewald error estimate: 0.2147E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
Please suggest me where I am wrong..
Thanks
Hirdesh
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Received on Fri Jan 28 2011 - 06:00:06 PST
