Dear Case£º
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
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sun Nov 06 2011 - 23:00:03 PST
