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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Received on Sun Nov 06 2011 - 19:30:02 PST
