VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Nov 07 2006 - 17:29:49 CST

Dear VMD community,
  I am performing FEP calculation where I transform one molecule into
another. I set a step size of 0.1 from 0 to 1 and perform 3000 steps of
equilibration and 6000 steps of data collection. My energy, Delta(E), starts
to increase and then reach 99999999 in the first 1120 of 3000 steps.
Delta(G) also shoots to 99999999 after 3000 steps. Here is a snapshot of my
initial and final energy states.

# STEP
Elec vdW dE
dE_avg Temp dG
# l l+dl
l l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.1
FepEnergy: 0 -19226.7021 -19226.5151 3394.0976
3394.0538 0.1432 0.1432 300.1763 0.1432
FepEnergy: 5 -19545.8269 -19545.6427 2154.4347
2154.6181 0.3677 0.2290 402.4467 0.2242
FepEnergy: 10 -19754.1355 -19754.0784 2356.6796
2357.0485 0.4260 0.3263 394.0959 0.3135
...
....
.....
FepEnergy: 2980 -22292.6723 -22296.4084 3020.5807
99999999.9999 99999999.9999 99999999.9999 301.8140 3.5073
FepEnergy: 2985 -22318.5017 -22321.7304 3026.9995
99999999.9999 99999999.9999 99999999.9999 300.7603 3.5083
FepEnergy: 2990 -22333.6021 -22339.4816 3009.8127
99999999.9999 99999999.9999 99999999.9999 304.7155 3.5093
FepEnergy: 2995 -22269.2559 -22280.2022 2991.7361
99999999.9999 99999999.9999 99999999.9999 300.5745 3.5103
#3000 STEPS OF EQUILIBRATION AT LAMBDA 0 COMPLETED
#STARTING COLLECTION OF ENSEMBLE AVERAGE
FepEnergy: 3000 -22271.6336 -22282.7764 2968.7255
99999999.9999 99999999.9999 99999999.9999 302.6601 99999999.9999
FepEnergy: 3005 -22311.0448 -22320.7037 2963.8890
99999999.9999 99999999.9999 99999999.9999 308.5868 99999999.9999
FepEnergy: 3010 -22160.5006 -22170.1657 2927.7686
99999999.9999 99999999.9999 99999999.9999 297.2231 99999999.9999

Finally the simulation ended prematurely giving this error:

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6000
WRITING COORDINATES TO DCD FILE AT STEP 6000
WRITING COORDINATES TO RESTART FILE AT STEP 6000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 6000
FINISHED WRITING RESTART VELOCITIES
TCL: Setting parameter lambda to 0.1
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 2 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.26461e-15 AT 0.0441942
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 16384 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 5.05845e-15 AT 0.0441942
TCL: Setting parameter lambda2 to 0.2
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 2 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.26461e-15 AT 0.0441942
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 16384 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 5.05845e-15 AT 0.0441942
TCL: Running for 6000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 156!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 119!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================

I am using Amber format prmtop and inpcrd files and not CHARMM format
*.psf/pdb files. So, I can not specify the atoms that should be excluded as
described in the tutorial for alchemical free energy calculation. I doubt if
my exclusion-list (that I produced after altering the EXLUCION_LIST in Amber
prmtop file to mutually exclude the atoms from the two molecules) is being
read in during simulation by NAMD. Is there a way to see if the atoms from
the two molecules are mutually excluded?
Although, in the log file, the number of exclusions is correctly specified.

Is there a way to specify the atoms that should be mutually excluded from
one another (say, by writing this information in a separate and mentioning
it in NAMD conf file)?

Could there be another reason for this kind of observation?

Thanks a lot in advance,
Rgds,
Nitin