Hi, All,
I am using Gibbs Dynamically Modified Windows method to perturb a VAL
analog ( without any partial charge ) into nothing in water. INTR = 46 is
used to make the molecule rigid, and NTR = 1 with factor 50. But when
lambda moved to 0.15 (from 1), Gibbs terminated with the error message:
ERROR TERMINATION DUE TO SHAKE OR TORCON
I tried to restart it but failed with same message. So, could anybody
tell me how I can restart my job?
(By the way, it can be restarted with INTR=0, but I need INTR=1.)
Following is the input and part of output file:
# Thermodynamic integration with dynamic windows.
&cntrl
irest = 1, ntx = 7, init = 4,
ntt = 1,
ntb = 2, ntp = 1, temp0 = 300.0,
ntf = 2, ntc = 2, tol = 0.0001, tolr2 = 0.0001
scee = 1.2,
nstlim = -1, dt = 0.001,
ielper = -1, idsx0 = 200,
idifrg = 1, intprt = 0,
almda = 1, isldyn = -2, amxmov = 0.02, amxrst = 0.1, dlmax = 0.025,
nstmeq = 40000, nstmul = 40000,
ntpr = 40000, isande = 1, ntwx = -1,
cut = 15., ntr = 1, intr = 46
&end
Hold the nucleic acid fixed
50.0
RES 1 1
END
END
00001 00002 00000 00000 00000 00000 00002 001.00000 000.00000
000.00000 999.00000 000.00000 999.00000 00000 00000
00001 00011 00000 00000 00000 00000 00002 001.00000 000.00000
000.00000 999.00000 000.00000 999.00000 00000 00000
00003 00004 00000 00000 00000 00000 00002 001.00000 000.00000
000.00000 999.00000 000.00000 999.00000 00000 00000
..............................
Current Lambda = 0.143248
Last F.E. update: Lambda = 0.150083 Step = 0 Method = T.I.
Accumulated "forward" quantities (Nonbond change)
Lambda = 0.150083 F_energy = 2.19930
Enthalpy = -255.09230 T*Entropy = -257.29160
(Note: values are unchanged from last report)
------------------------------------------------------------------------------
Routine TORCON (internal constraints) failed.
Required change is too large.
NITER = 1 Bond atom numbers are: 7 10
Current Lambda = 0.143248
Last F.E. update: Lambda = 0.150083 Step = 0 Method = T.I.
Accumulated "forward" quantities (Nonbond change)
Lambda = 0.150083 F_energy = 2.19930
Enthalpy = -255.09230 T*Entropy = -257.29160
ELEC = 0.000 NONB = 2.199 14NB = 0.000
14EL = 0.000 BADH = 0.000
Quantities used in integration:
<dV/d_lam> = 2.4782850 <V(lam-dep.)> = 60.637060
<V(lam-indep.)> = -6356.2590 <V(lam-dep)*dV/d_lam> = 186.64760
<V(lam-indep)*dV/d_lam> = -15785.460
------------------------------------------------------------------------------
NO DYNAMICALLY MODIFIED WINDOWS COLLECTED SINCE LAST REPORT
Routine Sec %
----------------------------
| Pairlist 1.45 0.91
| Nonbond 154.12 96.48
| Bond 0.02 0.01
| Angle 0.04 0.03
| Dihedral 0.07 0.04
| PMF 0.00 0.00
| Constraint 2.86 1.79
| Other 1.18 0.74
| Nonsetup 159.71 99.98
----------------------------
| Total 159.74 0.04 Hours
| Setup wallclock_t 0 seconds
| Nonsetup wallclock_t 161 seconds
***** ERROR TERMINATION DUE TO SHAKE OR TORCON *****
-----------------------------------------------------------------------
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Received on Wed Mar 23 2005 - 05:53:00 PST
