You can also use this file for slow heating...also, when you use restraints
ie. ntr =1, a reference coordinate is required as input...(-ref flag)..use
the same you are using with -c
Heating the system linearly with weak restraints
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 12,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0, nmropt=1,
nstlim = 50000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
&wt TYPE='TEMP0', istep1=0, istep2=40000,
value1=0.1, value2=300.0, /
&wt TYPE='DUMPFREQ',ISTEP1=10, /
&wt TYPE='END' /
Keep protein fixed
5.0
RES 1 92
END
END
Hope this helps you
On Mon, Jan 24, 2011 at 12:45 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Hi All,
> I am trying gradually heat my system from 0K to 300K. When i put no
> restrain
> then it runs fine, but in case of restrain, it is showing some error.
> Below mentioned is my mdin file:
> Heating up the system equilibration stage 1
> &cntrl
> imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10.0, ntr
> = 1, ntc = 2, ntf = 2,
> ig = 209833, tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln =
> 1.0, nstlim = 300000, dt = 0.002,
> ntpr = 1, ntwx = 100, ntwr = 1000, nmropt=1
> /
> &wt
> type='TEMP0', istep1=0, istep2=20000, value1=0, value2=20,
> /
> &wt
> type='TEMP0', istep1=20001, istep2=40000, value1=20, value2=40,
> /
> &wt
> type='TEMP0', istep1=40001, istep2=60000, value1=40, value2=60,
> /
> &wt
> type='TEMP0', istep1=60001, istep2=80000, value1=60, value2=80,
> /
> &wt
> type='TEMP0', istep1=80001, istep2=100000, value1=80, value2=100,
> /
> &wt
> type='TEMP0', istep1=100001, istep2=120000, value1=100, value2=120,
> /
> &wt
> type='TEMP0', istep1=120001, istep2=140000, value1=120, value2=140,
> /
> &wt
> type='TEMP0', istep1=140001, istep2=160001, value1=140, value2=160,
> /
> &wt
> type='TEMP0', istep1=160001, istep2=180001, value1=160, value2=180,
> /
> &wt
> type='TEMP0', istep1=180001, istep2=200000, value1=180, value2=200,
> /
> &wt
> type='TEMP0', istep1=200001, istep2=220001, value1=200, value2=220,
> /
> &wt
> type='TEMP0', istep1=220001, istep2=240000, value1=220, value2=240,
> /
> &wt
> type='TEMP0', istep1=240001, istep2=260001, value1=240, value2=260,
> /
> &wt
> type='TEMP0', istep1=260001, istep2=280000, value1=260, value2=280,
> /
> &wt
> type='TEMP0', istep1=280001, istep2=300000, value1=280, value2=300,
> /
> &wt
> type='END'
> /
> Keep Protein fixed with weak restraints
> 10.0
> RES 1 336
> END
> END
>
>
> The error which I am getting in output file is:
>
>
> ----- READING GROUP 1; TITLE:
> Keep Protein fixed with weak restraints
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
> GRP 1 RES 1 TO 336
> Number of atoms in this group = 5326
> ----- READING GROUP 2; TITLE:
> END
>
>
> rfree: End of file on unit 5
>
>
> Please suggest me where I am wrong..
>
> Thanks,
> Hirdesh
> _______________________________________________
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>
--
--
SUNITA GUPTA
Member Research Staff
LeadInvent Technologies Pvt.Ltd
Biotech Centre, University of Delhi
South Campus, Benito Juarez Road,
New Delhi, Pin 110021
Email- sunita.leadinvent.com
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Received on Mon Jan 24 2011 - 01:30:02 PST
