just to make sure, do not use ntt=1 !!!!
use ntt=3, with gamma_ln maybe 1 to 10
and indeed, use ig=-1 always !
adrian
On 11/16/16 10:41 AM, Thakur, Abhishek wrote:
> Thank you Dave and Nguyen.
>
> I really appreciate you all for your help and it is really very useful and I have learn many things.
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Wednesday, November 16, 2016 5:11:24 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] HMassRepartition
>
> After trying all suggestions ( :D ), you (Abhishek) can try to validate
> your protocol by running dt=0.001 and dt=0.004 (with hmass repartitioning)
> for tiny system (e.g Ala3) to get converge data (about few hundreds ns),
> then histogram CA distance between residue 1 and 3.
>
> If two runs (dt=0.001, dt=0.004) produce similar distribution, your
> protocol is fine.
>
> Hai
>
> On Wed, Nov 16, 2016 at 11:04 AM, David Cerutti <dscerutti.gmail.com> wrote:
>
>> If your nstlim is that high then you are not in serious danger from random
>> seed bugs. The problem is that the NET force imparted to each particle by
>> Langevin thermostating tends towards zero as 1/sqrt(nstlim). If nstlim is
>> 10000 you'll see a big problem, 100000 you'll see a problem but may not
>> notice it, and 1000000+ the effect is negligible. Still, ig = -1 is
>> usually a good policy unless you are intent on exactly reproducing a
>> trajectory, it which case you should set ig to a specific sequence of
>> numbers (i.e. 8572, 8573, 8574, ...) for each segment.
>>
>> Dave
>>
>>
>> On Wed, Nov 16, 2016 at 10:58 AM, Elvis Martis <elvis_bcp.elvismartis.in>
>> wrote:
>>
>>> Hi,
>>> I guess you must first try what Daniel and Dave have suggested, maybe
>> you
>>> can play around with the gamma_ln values later when you rule out
>> everything
>>> else.
>>> all the best.
>>>
>>> Regards
>>>
>>> *Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
>>> [image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in
>>>
>>> Website: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.elvismartis.in&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=l2AD0u80JBcrDncJrvGbeyRWbrcuSle1WUwNiPk_SQo&s=z1LHzlRTysm7lJjdu1yi13MT90BhQvMHYL-ss-wqO1k&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.elvismartis.in_&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=l2AD0u80JBcrDncJrvGbeyRWbrcuSle1WUwNiPk_SQo&s=ozH-R5w37tquEoHurrqtRmPfrXMvFJXhzexyVAnulxw&e= >
>>> group website: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.profeccoutinho.net.in_&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=l2AD0u80JBcrDncJrvGbeyRWbrcuSle1WUwNiPk_SQo&s=Rnvezi-CEpeB_p9I9o_SX3ZTLuSnZlmgLgRCOfEwbnk&e=
>>> Address:
>>>
>>> Kalina, Santa Cruz [E]
>>> , Mumbai, 400 098, INDIA
>>>
>>> Alt. e-mail: emartis12.live.com
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__in.linkedin.com_in_elvisadrianmartis&d=DgIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=l2AD0u80JBcrDncJrvGbeyRWbrcuSle1WUwNiPk_SQo&s=vGSGEFrKKkkA2P4D9yYWqUEm8s6yQmSHA6SuUALeMBs&e= >
>>>
>>>
>>> On 16 November 2016 at 21:25, Thakur, Abhishek <axt651.miami.edu> wrote:
>>>
>>>> Elvis thank you for such a quick response I am using default value for
>>>> gama_ln. so I guess it must be 0. Do you suggest someother value that I
>>>> should define>
>>>>
>>>>
>>>> David I don't think that I am using ig=-1, do you recommend me to try
>>> with
>>>> that?
>>>>
>>>>
>>>>
>>>> This is the script I am using in both case,
>>>>
>>>> Just with the difference of time step
>>>>
>>>>
>>>> imin=0,irest=1,ntx=5,
>>>> nstlim=2500000,dt=0.004,
>>>> ntf=2,ntc=2,ntb=0,
>>>> igb=8,cut=9999.0,rgbmax=25.0,
>>>> ntpr=500, ntwx=500, ntwr=10000,
>>>> saltcon=0.2,
>>>> temp0=300.0,
>>>> ntt=1,tautp=1.0,
>>>> nscm=0,ntxo=2,
>>>>
>>>>
>>>>
>>>> ________________________________
>>>> From: David Cerutti <dscerutti.gmail.com>
>>>> Sent: Wednesday, November 16, 2016 4:46:06 AM
>>>> To: AMBER Mailing List
>>>> Subject: Re: [AMBER] HMassRepartition
>>>>
>>>> These are both very short runs, and without knowing any other details
>>>> (assuming you have done everything correctly) I would expect the dimer
>> to
>>>> open with 1fs time steps soon enough. Just to make sure, are you
>> running
>>>> with a clock-based or otherwise varying random seed? I don't know what
>>> the
>>>> status of all our bulletproofing is, but if you're running with ascii
>>>> restarts then there could still be a way to get repeating pseudo-random
>>>> sequences into your system which would tend to unfold proteins if the
>>>> restarts occur frequently enough (or cause milder "opening" effects if
>>> the
>>>> restarts happen less frequently).
>>>>
>>>> Dave
>>>>
>>>>
>>>> On Wed, Nov 16, 2016 at 10:38 AM, Thakur, Abhishek <axt651.miami.edu>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have carried out two different GB/SA simulation, igb=5 and all the
>>>>> parameters same
>>>>>
>>>>> 1. With HMassRepartition with dt=0.004 and in 20ns I found that my
>>> dimer
>>>>> opened.
>>>>>
>>>>> 2.Simple Gb/SA with dt=0.001 and in 20ns I have found my dimer has
>> not
>>>>> moved at all.
>>>>>
>>>>>
>>>>> I cannot get the reason behind this, as both have same duration of
>>>>> simulation. Can this be possible or I have done some mistake>
>>>>>
>>>>>
>>>>>
>>>>> Thanking you,
>>>>>
>>>>> Abhishek
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Nov 16 2016 - 10:30:02 PST
