I see now that you are using langevin dynamics- did
you apply to bugfix for temperature changing with ntt=3?
(bugfix 25)
Manish Datt wrote:
>dear carlos
>the output has indeed read the weight changes but strangely it has not
>read in the tautp flag.
>what should be done to rectify this?
>
>Manish Datt
>Research Scholar
>Bioinformatics Centre
>Institute of Microbial Technology
>Sector 39A, Chandigarh-160036
>India.
>
>
>On Fri, 7 Oct 2005, Carlos Simmerling wrote:
>
>
>
>>does the output say that is has read the weight changes?
>>read the top portion (up to step 1 energies) carefully as
>>it should verify the weight changes assigned.
>>also you might need tighter coupling (smaller tautp)
>>to enforce the ramping at the rate you want.
>>
>>
>>
>>Manish Datt wrote:
>>
>>
>>
>>>hi all
>>>i`m trying to run md on a protein-dna complex with following input
>>>dynamcis 300000
>>>&cntrl
>>> imin=0, irest=0, ntx=1, nstlim=300000, dt=0.001,
>>> drms=0.01, ntb=0, cut=999, ntpr=10, ntwx=100, ntwr=100, ntt=3,
>>> igb=1, ntr=0, nmropt=1, tautp=1.5, gamma_ln=1, tempi=0, temp0=30
>>>/
>>>&wt
>>> type='TEMP0', istep1=0, istep2=10000,
>>> value1=0.0, value2=10.0
>>>&end
>>>&wt
>>> type='TEMP0', istep1=10001, istep2=20000,
>>> value1=10.0, value2=20.0
>>>&end
>>>&wt
>>> type='TEMP0', istep1=20001, istep2=30000,
>>> value1=20.0, value2=30.0
>>>&end
>>>&wt
>>>type='END'
>>>&end
>>>
>>>now the problem is that the temperature crossess 10k after 0.27ps, while
>>>as per weights given the temperature should reach 10k after 10ps.
>>>moreover identical output was obtained when no weights were specified.
>>>i`m absolutely clueless on how to interpret my results. is theresomething
>>>that i`m missing out?
>>>any guidance on how to control temperature change would be
>>>highly
>>>appreciated.
>>>
>>>regards,
>>>
>>>Manish Datt
>>>Research Scholar
>>>Bioinformatics Centre
>>>Institute of Microbial Technology
>>>Sector 39A, Chandigarh-160036
>>>India.
>>>
>>>
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>
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
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Received on Sat Oct 08 2005 - 12:53:00 PDT
