Re: gaussian aMD with iE=2 (setting E threshold at maximum)

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Sun Jan 27 2019 - 06:00:02 CST

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 <http://mpi-muenster.mpg.de>
>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mpi-muenster.mpg.de%2F43241%2Fcojocaru&amp;data=02%7C01%7Cmiao%40ku.edu%7C5789d5fa46ab4a359f5908d682ca4fea%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C636840202785027668&amp;sdata=tIFFaAcVKhniZY%2Bt1VX%2FwOGxL4MtcBu3ildWX%2Fp0FCU%3D&amp;reserved=0
>>
>

-- 
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://www.mpi-muenster.mpg.de/43241/cojocaru

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