”Third, 500 is too strong a force constant for most purposes. Consider
using
a value about two orders of magnitude smaller.“
If I want to keep Graphene sheet Constrain in the MD simulaiton, is 500
still too much? I dont quite understand.
THanks
haiya
在 2011年11月7日 下午2:30，hai wei <weihy61.gmail.com>写道：
> Dear Case：
>
> DO I have to set *nscm=0 *in the control. Since I am reading one of the
> old post, says that "*One thing to try is *
> *> make sure you set nscm=0 when doing Belly runs*"
>
> ***> *
> *> I thought I would add my 2c to this discussion. Firstly I just want to
> give *
> *> a caution with regards to the use of ibelly. That is that you really
> not use *
> *> it!!! It simply zeros the forces and is in no way correct or physical.
> *
> *> Especially if you start doing things like NPT simulations with it. In
> this *
> *> case your virial will be wrong, you pressure will be wrong and thus
> your *
> *> density will be wrong. If you must restrain things then you should
> probably *
> *> use harmonic restraints. *
> *> *
> *> Note, things like seeing a 200K temperature drop on the first step
> makes *
> *> sense with using belly for such a huge portion of your syste, If you
> are *
> *> starting from a restart file where things were not frozen and then you
> *
> *> suddenly freeze a chunk of it you have just magically destroyed a ton
> of *
> *> kinetic energy... *
> *> *
> *> With regards to the problems you are seeing this could be because of
> all *
> *> sorts of issues including trying to do NPT with ibelly. One thing to
> try is *
> *> make sure you set nscm=0 when doing Belly runs, Sander may be doing
> this *
> *> while pmemd is not. Second make sure you do not try to use langevin
> dynamics *
> *> (ntt=3) with ibelly since it will likely not work. *
> *> *
> *> All the best *
> *> Ross *
>
> THanks.
>
> haiya
>
>
> 2011/11/7 hai wei <weihy61.gmail.com>
>
>> Dear Case:
>>
>> Thanks for your reply, and apologize for the unclear mail I send, My
>> system is compsed of Protein (res number 1 582), Graphene (res number 583
>> 605) and counterion and water.
>>
>> I am doing simulaiton as following step:
>>
>> 1, minimization of the system:
>> &cntrl
>> imin = 1, maxcyc = 2500, ncyc = 1000, ntb = 1, ntr =
>> 1, cut = 10,
>> /
>> Hold the protein and graphen sheet fixed
>> 500.0
>> RES 1 605
>> END
>> END
>>
>> 2. Heating the system to 360K:
>> &cntrl
>> imin = 0, irest = 0, ntx = 1, ntp = 0, ntb = 1,
>> cut = 10,
>> ibelly = 1,
>> ntc = 2, ntf = 2, tempi = 0.0, temp0 = 360.0,
>> ntt = 2, (ibelly does not work with ntt=3,)
>> gamma_ln = 1.0, nstlim = 10000, dt = 0.002, ntpr = 250, ntwx = 250,
>> ntwr = 10000,
>> iwrap = 1, ioutfm=1, nscm = 100, /
>>
>> Keep protein and Graphen sheet fiexed with ibelly
>> RES 1 605
>> END
>> END
>>
>> 3. 1ns MD simulation at 360K ;
>> &cntrl
>> imin = 0, irest = 1, ntx = 5, ntb = 2, pres0 = 1.0, ntp = 1, taup =
>> 2.0, cut = 10,
>> ibelly = 1,
>> ntc = 2, ntf = 2, tempi = 360.0, temp0 = 360.0,
>> ntt = 2,
>> gamma_ln = 1.0, nstlim = 500000, dt = 0.002, ntpr = 250, ntwx = 250,
>> ntwr = 10000,
>> nscm = 100, ioutfm = 1, iwrap=1,
>> /
>> Keep protein and Graphen sheet fiexed with ibelly
>> RES 1 605
>> END
>> END
>>
>> 4. cooling the system to 300k ;
>> &cntrl
>> imin = 0, irest = 1, ntx = 5, ntp = 0, ntb = 1,
>> cut = 10,
>> ibelly = 1,
>> ntc = 2, ntf = 2, tempi = 360.0, temp0 = 300.0,
>> ntt = 2,
>> gamma_ln = 1.0, nstlim = 100000, dt = 0.002, ntpr = 250, ntwx = 250,
>> ntwr = 10000,
>> iwrap = 1, ioutfm=1, nscm = 100,
>> /
>> Keep protein and Graphen sheet fiexed with ibelly
>> RES 1 605
>> END
>> END
>>
>> 5. MD production run at 300k ;
>> &cntrl
>> imin = 0, irest = 1, ntx = 5, ntb = 2, pres0 = 1.0, ntp = 1, taup =
>> 2.0,
>> cut = 10,
>> ntr = 0,
>> ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0,
>> ntt = 2,
>> gamma_ln = 1.0,
>> nstlim = 500000, dt = 0.002, ntpr = 250, ntwx = 250, ntwr = 10000,
>> nscm = 100, ioutfm = 1, iwrap=1,
>> /
>> Keep graphene sheet fixed with ibelly
>> RES 583 605
>> END
>> END
>>
>> After I read the ambermail list of ibelly question, like, not work with
>> ntt=3, pememd not work, I think the above control should run normally.
>>
>> While I still got a problem here, when I heat the system, How to just put
>> a weak restrain force on protein , while keep graphene sheet ibelly
>> constrain, Since ntr=1, and ibelly=1 can not be used at the same time.
>>
>> THanks.
>>
>> haiya
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 2011/11/7 case <case.biomaps.rutgers.edu>
>>
>>> On Mon, Nov 07, 2011, hai wei wrote:
>>> >
>>> > I am runing a MD simulation with protein on top of Graphene sheet,
>>> During
>>> > the simulaiton, I try to fix the graphene sheet while adding the
>>> following
>>> > input:
>>> >
>>> > hold the protein fixed
>>> > 500.0
>>> > RES num1 num2
>>> > END
>>> > END
>>> >
>>> > While I found that the Graphene sheet does not fixed as it should be,
>>> There
>>> > are still some ripples shown.
>>>
>>> First, the comment indicates that you are holding the *protein* fixed,
>>> whereas
>>> your email text indicates that you wish to keep the graphene fixed.
>>> Without
>>> knowing anything about your system (and not knowing what num1 and num2
>>> are),
>>> I can't tell what should be happening.
>>>
>>> Second, you also need to set ntr=1 in the &cntrl namelist; otherwise
>>> lines
>>> like those above will be ignored. The output will summarize the
>>> restraints,
>>> and tell you how many atoms were involved. If there is nothing in the
>>> about
>>> about restrained atoms, you need to re-examine your inputs.
>>>
>>> Third, 500 is too strong a force constant for most purposes. Consider
>>> using
>>> a value about two orders of magnitude smaller.
>>>
>>> ...good luck....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Sun Nov 06 2011 - 23:30:02 PST
