Dear Amber users;
1) Is it necessary that Etot should be negative .... I have seen in
most of the querries and tutorial output, that Etot is negative.
I used the following input for equilibrium phase after heating from 0 - 300K
here is equilibrium input:
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
these last steps energy output values
NSTEP = 99900 TIME(PS)
= 249.800 TEMP(K) =
295.30 PRESS = -56.5
Etot = 6133.5908
EKtot = 3811.4443
EPtot =
2322.1465
BOND =
635.3000 ANGLE =
1956.2672 DIHED
= 405.6718
1-4 NB = 195.6267 1-4
EEL = 4000.9903
VDWAALS = -4121.3236
EELEC = -750.3858
EHBOND =
0.0000 RESTRAINT
= 0.0000
EKCMT = 673.1555
VIRIAL = 788.8184
VOLUME = 94811.4804
Density
= 1.2381
Ewald error estimate: 0.5658E-03
------------------------------------------------------------------------------
NSTEP = 100000 TIME(PS)
= 250.000 TEMP(K) =
299.31 PRESS = 59.6
Etot = 6178.0066
EKtot = 3863.0849
EPtot =
2314.9217
BOND =
674.1848 ANGLE =
1878.4011 DIHED
= 425.5195
1-4 NB = 189.5570 1-4
EEL = 4010.5437
VDWAALS = -4097.2245
EELEC = -766.0599
EHBOND =
0.0000 RESTRAINT
= 0.0000
EKCMT = 685.0976
VIRIAL = 563.0999
VOLUME = 94823.4042
Density
= 1.2380
Ewald error estimate: 0.1530E-03
Is there anything wrong in starting structures or input files??
please suggest
thanks and regards;
Jiomm
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Received on Sun Nov 15 2009 - 21:30:02 PST
