From: Fabio Passetti (passetti_at_inca.gov.br)
Date: Wed Sep 05 2007 - 07:41:39 CDT
Dear all,
I am experiencing the same problem. Any insights about this topic is
really useful.
Regards,
Fabio
owner-namd-l_at_ks.uiuc.edu escreveu:
> hii!!
> can you just write your conf file here the last part of the run?There
> might be some problem in going from 300K to 500K.
> regards,
> monika
> Arun Krishnan wrote:
>> Dear NAMD list users,
>>
>> I have been trying to carry out unfolding simulations of Ubqiuitin. I
>> use the top_all22_prot.inp and par_all22_prot.inp topology and
>> parameter files.
>> I did the following steps:
>>
>> a) Energy minimization
>> b) Heating to 300K
>> c) Equilibration for 50ps NPT
>> d) Production run @300K for 1ns. NPT
>> e) Heating to 500K
>> f) Equilibration for 50ps NPT
>> g Production run @500K for 12ns NPT
>>
>> Very surprisingly, I don't see the RMSD values changing (with respect
>> to the final equilibrated frame at 300K) by greater than 4-5
>> Angstroms. This is very weird. There is a paper in Physical Review E,
>> 72, 051928, 2005 "Unfolding dynamics of the protein ubiquitin:
>> Insight from simulation" where they achieved drastic unfolding within
>> 1ns
>> for ubiquitin at 520K. I followed what they did and tried at 520K too.
>>
>> I have used NPT throughout.. but I also used NVT and NVE ensembles..
>> and in all cases it seems to be very stable. Does anyone have any
>> pointers to what I might be doing wrong?
>>
>> Thanks in Advance,
>>
>> Arun
>> -
>> ------------------------------------------------------------------------
>>
>> Internal Virus Database is out-of-date.
>> Checked by AVG Free Edition. Version: 7.5.472 / Virus Database:
>> 269.8.0/817 - Release Date: 5/24/2007 4:01 PM
>>
>
>
>
>
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