Dear Amber,
When I run a TI job, the energy doesn't seem to conserve in each clambda
step in no matter step 1, step 2 (soft core potential step) and step 3.
The total energy always drops significantly at the beginning of each stage
(minimization, constant volume equilibrium, constant
pressure equilibrium and production run). Moreover, when MD enters into a
QMMM production run, the total energy will drop again and then reach a
higher value than the total energy of minimization and equilibrium. Please
see the following Xmgrace figures for more details.
*TI_energy<
http://i1076.photobucket.com/albums/w454/happypsu4/TI_energy.png>
(**
http://i1076.photobucket.com/albums/w454/happypsu4/TI_energy.png**)*
*TI_pressure<
http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png>(
http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png)*
*TI_temperature<
http://i1076.photobucket.com/albums/w454/happypsu4/TI_temperature.png>(
http://i1076.photobucket.com/albums/w454/happypsu4/TI_temperature.png)*
The following is my Amber TI script in step 1 (to simplify, I just show
half of the script, as in a group ):
mask0=':MAA.F14,CL17'
mask1=
for X in 1,2,3
do
###################### minimization step ################################
imin = 1,
maxcyc = 2000,
ntmin = 2,
ntpr = 100,
ntf = 2,
ntc = 1, (I also tried ntc=2 here)
ntb = 1,
cut = 10.0,
icfe = 1,
clambda = 0.${X},
ifsc=0,
crgmask='${mask0}',
&end
###########################Constant volume equilibrium to equilibrate
temperature ######################################
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.001,
ntpr = 250,
ntwx = 250,
ntwr = 2500,
icfe = 1,
clambda = 0.${X},
ifsc=0,
crgmask='${mask0}',
/
Keep the Protein fixed with weak restraints
10.0
RES 1 258
/
END
##################################### Constant Pressure equilibrium to get
a proper density #########################
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
pres0 = 1.0,
ntp = 1,
taup = 2.0,
cut = 10,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.001
ntpr = 250,
ntwx = 250,
ntwr = 2500,
icfe = 1,
clambda = 0.${X},
ifsc=0,
crgmask='${mask0}',
&end
############################QMMM production
run###############################################
imin = 0,
ntx = 5,
irest = 1,
ntb = 2,
ntp = 1,
pres0 = 1.0,
taup = 2.0,
ntf = 1,
ntc = 1,
cut = 10.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000,
dt = 0.001,
ntpr = 250,
ntwr = 2500,
ntwx = 250,
icfe=1,
clambda = 0.${X},
ifsc=0,
crgmask='${mask0}',
ifqnt = 1
/
&qmmm
iqmatoms= 3868,3869,3870,3871,3872,
3873,3874,3875,3876,3877,
3878,3879,3880,3881,3882,
3883,3884,3885,3886,3887,
3888,3889,3890,1395,1394,
1396,1398,1399,2328,2327,
3833,3834,3835,3836,3837,
3838,3839,3840,3841,3862,
3863,3864,3865,3866,3867,
qmchage=-1,
qm_theory='PM3',
qmshake=0,
qm_ewald=1,
qm_pme=1,
/
&end
############################################################################
I have tried
a. turn off QMMM. Or keep QMMM but with qmshake=1,. The same issue
b. Run in both Amber 11 & 12, The same issue
c. Turn on / off SHAKE. The same issue.
d. Turn off Langevin Dynamic. The same issue
e. Switch to Andersen temperature control. The same issue.
f. Prepare new .prmtop and .inpcrd files and run again. The same issue
g. I have set ntpr=1 and check all the .out files by "gvim -d" and total
energies, temperature, pressure and all the MM components are the same in
the same group file.
h. The restart files from V0 to V1 are identical.
I only tried 9 windows so far.
clambda = 0.${X}, for X in 1 2 3 4 5 6 7 8 9
But I guess number of windows is not the issue here.
Please let me know if any comment. Many comments.
Henry
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Received on Fri Aug 03 2012 - 11:00:04 PDT
