Dear Amber users,
I’ve been following tutorial A10 in order to perform SMD for my protein and its ligand using the LCOD method. In the tutorial, the spring constant for the proton transfer to occur is set to 1000 kcal/mol whose value, according to a few related questions on the mailing list, is too high.
In order to find a reasonable value, I’ve run the simulation several times and the proton transfer takes place for “low” values such as 10 kcal/mol if the output_freq is set to 1000, like in the tutorial. But, if the output_freq is lowered (I’ve tried 500 and 50) the proton transfer doesn’t occur anymore (for harm=10kcal/mol).
Moreover, in the output_file .txt the CV, handle_position and work are not the same for a given time during the MD, resulting in different values for the total work done.
For harm=10 kcal/mol and output_freq=1000 I obtain:
#
# MD time (ps), CV, handle_position, spring_constant, work
#
925.0000 0.50139387 0.70000000 10.00000000 0.00000000
925.5000 0.89660018 0.69958280 10.00000000 0.00030631
926.0000 0.83105576 0.69834240 10.00000000 0.00081418
926.5000 0.66819394 0.69629560 10.00000000 0.00204283
927.0000 0.60709575 0.69345920 10.00000000 0.00467988
927.5000 0.93546672 0.68985000 10.00000000 0.00719652
928.0000 0.56761201 0.68548480 10.00000000 0.01073920
928.5000 0.62737834 0.68038040 10.00000000 0.01357336
929.0000 0.92623955 0.67455360 10.00000000 0.01711340
929.5000 0.66861857 0.66802120 10.00000000 0.02039487
930.0000 0.91611501 0.66080000 10.00000000 0.02901486
...
#
# <> total work done: 0.7690942380
For harm=10 kcal/mol and output_freq=500 I obtain:
#
# MD time (ps), CV, handle_position, spring_constant, work
#
925.0000 0.50139387 0.70000000 10.00000000 0.00000000
925.2500 0.80711710 0.69989535 10.00000000 0.00022605
925.5000 1.00173702 0.69958280 10.00000000 0.00094337
925.7500 0.81672099 0.69906445 10.00000000 0.00198729
926.0000 0.81074280 0.69834240 10.00000000 0.00416796
926.2500 0.93641120 0.69741875 10.00000000 0.00658384
926.5000 0.79972556 0.69629560 10.00000000 0.00872512
926.7500 0.88288670 0.69497505 10.00000000 0.01112337
927.0000 0.99659450 0.69345920 10.00000000 0.01380751
927.2500 0.91748709 0.69175015 10.00000000 0.01664516
927.5000 0.98411987 0.68985000 10.00000000 0.01972750
927.7500 0.76115131 0.68776085 10.00000000 0.02316773
928.0000 0.82942938 0.68548480 10.00000000 0.02737620
928.2500 0.74668613 0.68302395 10.00000000 0.03189408
928.5000 0.95082231 0.68038040 10.00000000 0.03673629
928.7500 0.79738517 0.67755625 10.00000000 0.04177707
929.0000 1.03951245 0.67455360 10.00000000 0.04712890
929.2500 0.71139449 0.67137455 10.00000000 0.05324293
929.5000 0.85144838 0.66802120 10.00000000 0.05961067
929.7500 0.92964077 0.66449565 10.00000000 0.06619512
930.0000 0.84766718 0.66080000 10.00000000 0.07329916
...
#
# <> total work done: 11.2413859667
So I wonder what exactly the output_freq achieves during the SMD? As I want to run the same kind of simulation for my protein and its ligand, I’d like to know how to choose this value.
Thank you for any insight on this subject,
Sincerely,
Ruth
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Received on Thu Nov 24 2016 - 04:00:03 PST
