From: Miao, Yinglong (miao_at_ku.edu)
Date: Mon Jan 28 2019 - 09:02:37 CST
Dear Vlad,
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: Tue Dec 31 2019 - 23:20:27 CST
Andrew (CCed) has implemented a new algorithm to calculate potential statistics and then GaMD acceleration parameters, which allows iE=2 simulations of most protein systems. We are trying to incorporate it into the latest NAMD code. Hope that will be ready for your use soon …
Best,
Yinglong
Yinglong Miao, Ph.D.
Assistant Professor
Center for Computational Biology and
Department of Molecular Biosciences
University of Kansas
http://miao.compbio.ku.edu
On Jan 27, 2019, at 6:00 AM, Vlad Cojocaru <vlad.cojocaru_at_mpi-muenster.mpg.de<mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
Dear Yinglong,
Thanks .. OK, I see, I was just confused by the warning being printed after the values .. But yes, you are right k0 is > 1 ... Going back to theory, it seems that to keep k0 under 1, I would need to increase sigma0 to about 15 for the boost on dihedral potential and 150 for the boost on the total potential ....
I guess these values maybe way too big for reweighting, so iE=2 may not be an option at all for my system ... Right ?
Best,
Vlad
On 1/26/19 8:23 PM, Miao, Yinglong wrote:
Dear Vlad,
It sounds great that you are trying the iE=2 mode. Those values with k0<1 may be calculated after iE was switched to 1 (lower bound for reference energy E), but they may be greater than 1 with iE=2, for which the values were not output in the log file.
All the best,
Yinglong
Yinglong Miao, Ph.D.
Assistant Professor
Center for Computational Biology and
Department of Molecular Biosciences
University of Kansas
http://miao.compbio.ku.edu
On Jan 25, 2019, at 7:32 AM, Vlad Cojocaru <vlad.cojocaru_at_mpi-muenster.mpg.de<mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
Dear all,
We are doing some testing using the gaussian accelerated MD implemented in NAMD. When running with iE=2 (setting the threshold potential at its maximum value), as soon as the simulation switched from the classical MD equilibration to gaussian accelerated MD (step 5000000 in this particular case), I get the warning below. The warning says that k0 > 1 and that is why the simulation switches automatically to iE=1. However, according to the output k0 is 0.43 for the boost on the dihedral energy and 0.05 for the boost on the total potential (see below). These are both below 1 ....
I'd appreciate a lot if somebody could explain whether this is a bug or am I overlooking something.
Thanks a lot
Best wishes
Vlad
----sample output -----
ACCELERATED MD: STEP 5000000 dV 34.5194 dVAVG 0.0138077 BOND 1320.89 ANGLE 3054.73 DIHED 4612.83 IMPRP 0 ELECT -1.15509e+06 VDW 172575 POTENTIAL -973530 LJcorr -3898.48
GAUSSIAN ACCELERATED MD: DIHED iE 1 Vmax 4740.73 Vmin 4477.74 Vavg 4602.2 sigmaV 26.2707 E 4740.73 k0 0.433587 k 0.0016487
GAUSSIAN ACCELERATED MD: DIHED !!! WARNING: k0 > 1, SWITCHED TO iE = 1 MODE !!!
GAUSSIAN ACCELERATED MD: TOTAL iE 1 Vmax -975387 Vmin -984730 Vavg -977593 sigmaV 490.889 E -975387 k0 0.0517528 k 5.53917e-06
GAUSSIAN ACCELERATED MD: TOTAL !!! WARNING: k0 > 1, SWITCHED TO iE = 1 MODE !!!
--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmpi-muenster.mpg.de&data=02%7C01%7Cmiao%40ku.edu%7C42a7eee54e96497c59af08d6844ef99b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C636841872094003229&sdata=R6OpMEE6gnGnhsFaro6wHFW2ElL8cI36vMMsOQhq89M%3D&reserved=0>
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--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de<http://mpi-muenster.mpg.de>
http://www.mpi-muenster.mpg.de/43241/cojocaru