Date: Thu, 31 Jan 2013 17:37:29 -0600
Dear Amber,
We try to investigate whether simulation length will affect the mmP(G)BSA
accuracy and find the optimal simulation length of our system . After
50ps NVE equilibration with restraint and 50ps NPT equilibration without
restraint, we separate the NPT production with 4 pieces, 0.25 ns per
piece. Then the mmP(G)BSA calculation are performed for 0.25, 0.5, 0.75, 1
ns production run. In the production run, the 15A ligand region is
restraint to obtain a convergent RMSD due to the flexible nature of the
protein. Here is the question:
* In each 0.25 ns simulation, the system's potential energy will be lower
than the previous one (as shown in the attachment).* *The reason might be
because the restraint energy in each 0.25 ns simulation becomes lower than
the previous run.* Here are the average energy of 0.5~0.75 ns and 0.75~1
ns production run.
* 1. May we know the reason of decreasing restraint energy? *
*
*
* 2. May we know if mmP(G)BSA algorithm would include restraint energy
into molecular mechanics potential energy (dEmm) calculation? *
*500~750 ps*
NSTEP = 250000 TIME(PS) = 850.000 TEMP(K) = 299.92 PRESS =
2.6
Etot = -90610.3171 EKtot = 23354.8465 EPtot =
-113965.1635
BOND = 732.3907 ANGLE = 1982.9737 DIHED =
2673.9687
1-4 NB = 937.1613 1-4 EEL = 12685.5340 VDWAALS =
15140.6334
EELEC = -154806.9944 EHBOND = 0.0000 *RESTRAINT =
6689.1691*
EAMBER (non-restraint) = -120654.3327
EKCMT = 10200.2929 VIRIAL = 10179.6451 VOLUME =
372337.1599
Density =
1.0435
Ewald error estimate: 0.4059E-04
*750ps~1,000 ps *
A V E R A G E S O V E R 1000 S T E P S
NSTEP = 250000 TIME(PS) = 1100.000 TEMP(K) = 299.95 PRESS =
-2.6
Etot = -91286.4339 EKtot = 23357.5922 EPtot =
-114644.0261
BOND = 731.6874 ANGLE = 1977.4873 DIHED =
2677.3300
1-4 NB = 939.5516 1-4 EEL = 12704.9512 VDWAALS =
15308.5330
EELEC = -155434.4507 EHBOND = 0.0000 *RESTRAINT =
6450.8840*
EAMBER (non-restraint) = -121094.9101
EKCMT = 10202.1509 VIRIAL = 10223.3305 VOLUME =
371915.0679
Density =
1.0447
Ewald error estimate: 0.4120E-04
Here is our production setting
&cntrl
imin = 0,
ntx = 5,
irest = 1,
ntpr = 250,
ntwr = 2500,
ntwx = 250,
ntr = 1,
restraint_wt = 0.5,
restraintmask = ':324 >:15.0',
ntf = 2,
ntc = 2,
ntb = 2,
cut = 8.0,
nstlim = 250000,
dt = 0.001,
tempi = 300.0
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
ntp = 1,
pres0 = 1.0,
taup = 2.0,
ig = -1,
&end
Cheers,
Henry
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(image/jpeg attachment: mmPBSA_question_2.JPG)
