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

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon Jan 28 2019 - 09:26:31 CST

Thanks a lot.

Andrew, I'd appreciate a lot if you could let me know when that is ready
for a test on our systems.

Best
Vlad

On 1/28/19 4:02 PM, Miao, Yinglong wrote:
> Dear Vlad,
>
> 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 <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>
>>>> 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
>>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mpi-muenster.mpg.de%2F43241%2Fcojocaru&data=02%7C01%7Cmiao%40ku.edu%7C42a7eee54e96497c59af08d6844ef99b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C636841872094003229&sdata=SwUyou%2F8b2F2pzkbqm9%2BzpOs960ChwhzTQdtxqRl1zA%3D&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://mpi-muenster.mpg.de>
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
> 

-- 
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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