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Dear Amber users
I am running thermodynamic integration with amber, pmemd on cpu, Amber14. I am using the following input file for running:
TI simulation
&cntrl
imin = 0, nstlim = 150000, irest = 1, ntx = 5, dt = 0.002,
ntt = 3, temp0 = 298.0, gamma_ln = 5.0, ig = -1,
ntc = 2, ntf = 1, ntb = 1,ntp = 0,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 100, ntwr = 2000,
icfe = 1, ifsc = 1, clambda = 0, scalpha = 0.5, scbeta = 12.0,
logdvdl = 1,
ifmbar = 1, bar_intervall = 1000, bar_l_min = 0.0, bar_l_max = 1.0,
bar_l_incr = 0.1,
timask1 = ':116,149', timask2 = ':159,160',
scmask1 = ':116,149', scmask2 = ':159,160',
&end
The output is:
| TI region 2
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) =445092.95 PRESS = 0.0
Etot = ************** EKtot = 156924004.1488 EPtot = **************
BOND = 51767754.8751 ANGLE = 299843.0710 DIHED = 13000.8615
1-4 NB = ************** 1-4 EEL = -1193.9673 VDWAALS = **************
EELEC = ************** EHBOND = 0.0000 RESTRAINT = 404917.1072
EAMBER (non-restraint) = **************
DV/DL = **************
Ewald error estimate: 0.8890E+02
------------------------------------------------------------------------------
Softcore part of the system: 64 atoms, TEMP(K) = 273603.75
SC_Etot= 118913.0956 SC_EKtot= 52195.4965 SC_EPtot = 66717.5991
SC_BOND= 58641.9133 SC_ANGLE= 6255.7856 SC_DIHED = 248.7149
SC_14NB= 1571.4913 SC_14EEL= -51.8619 SC_VDW = 161.5745
SC_EEL = -110.0186
SC_RES_DIST= 2503.4585 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 6362.6956 SC_VDW_DER= *********** SC_DERIV = ***********
------------------------------------------------------------------------------
when I am using this input as "lambda=1" the system runs well. But when I switch to "lambda = 0" the system crashes with the following coordinates:
-2.2263528 0.4948044 1.3902758 -9.8532522 -20.0000000 4.7261966
6.1548176 20.0000000 3.7616364 4.3712168 0.3085792 -0.6998316
11.9788399 -20.0000000 -20.0000000 -20.0000000 20.0000000 20.0000000
3.6102063 2.5685121 -2.9439387 -2.4273888 -20.0000000 -20.0000000
20.0000000 10.4990634 20.0000000 -0.6574321 4.3513134 -1.9494082
15.8827264 -20.0000000 20.0000000 10.8980516 20.0000000 -20.0000000
-0.2922468 3.1186614 -4.0249280 -9.9457371 4.3672343 -20.0000000
12.1206371 -14.9312673 20.0000000 3.3266217 -1.5028986 1.1370716
-20.0000000 -12.9537867 -20.0000000 20.0000000 20.0000000 16.7487781
87.1893599 101.2862751 136.4590540 90.0000000 90.0000000 90.0000000
The system is very well minimized with "lambda=0" as follow:
minimisation
&cntrl
imin = 1, ntmin = 1, maxcyc = 600,ncyc =400,
ntpr = 20, ntwe = 20,
dx0 = 1.0D-7,
ntb = 1,
icfe = 1, ifsc = 1, clambda = 0, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':116,149', timask2 = ':159,160',
scmask1 = ':116,149', scmask2 = ':159,160',
!method 2:
!scmask1 = '', scmask2 = ':163.HG=',
/
&ewald
/
and the minimized system sounds without problem. I started the restart simulation from a previous run. With ntpr=1 also I have the same coordinate with "20000" from starting point in equillibration. Any idea why this happen when the lambda switch to 0?
Thanks
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Received on Thu Aug 06 2015 - 08:00:03 PDT
