From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Wed Sep 05 2007 - 12:19:13 CDT
I wonder if the pressure is an issue. I found it to be in some of my
simulations, and after going with a pressure of ~30 bars, it worked
fine (didn't try ubiquitin). I also did NVE simulations
(equilibrated at NPT). Also, if I remember correctly, different
groups have had different unfolding behavior for ubiquitin, so that
may be something to look into.
On Sep 5, 2007, at 8:37 AM, Peter Freddolino wrote:
> Hi Arun,
> you might just want to start by looking at the box volume (from the
> xst
> file), and how it varies with temperature. To get the water
> density, you
> need to take those box volumes and subtract the protein volume (I
> believe you can get this using MSMS, or from the server at
> http://molbio.info.nih.gov/structbio/basic.html). This should let you
> calculate the water density fairly easily. Large volume
> fluctuations in
> an NPT md simulation can do odd things to the dynamics, which is
> why I'm
> curious whether the volume varied as much in your case as it did in
> the
> paper you cited.
> Peter
>
> Arun Krishnan wrote:
>> Hi Peter,
>>
>> I did check the temperature.. and it was stable at around 518K...
>> also... interestingly, after my equilibration run
>> at 300K, I noticed that the temperature stabilized at around 298K...
>> would that lead to any problems?
>>
>> Also, how do I find out the water density? Can you explain that in
>> short please?
>>
>> Thanks,
>>
>> Arun
>>
>> On 9/5/07, *Peter Freddolino* < petefred_at_ks.uiuc.edu
>> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>>
>> Hi Arun,
>> have you, for example, plotted the temperature output from this
>> run to
>> verify that the temperature is stable and at 520K? I ask partly
>> because
>> I don't recall how namd interprets the string "520K" as a
>> floating
>> point
>> number; normally one would simply give the value in Kelvin, but
>> omit the
>> unit.
>>
>> Also, what average volume (or water density) do you see at 520K
>> compared
>> to the 300 K equilibration? It looks like some very large
>> fluctuations
>> were observed in the paper you cited, but they do not make it
>> clear what
>> method they used for pressure control.
>>
>> Best,
>> Peter
>>
>> Arun Krishnan wrote:
>>> Hi Monika,
>>>
>>> I have uploaded all my config files to my website. You can get them
>>> from here:
>>>
>>> a) energy minimization:
>>> http://www.iab.keio.ac.jp/~krishnan/downloads/min.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/min.namd>
>>> < http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/min.namd>
>>> b) heating to 300K:
>>> http://www.iab.keio.ac.jp/~krishnan/downloads/heating.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/heating.namd>
>>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/heating.namd>
>>> c) equilibration @300K:
>>>
>> http://www.iab.keio.ac.jp/~krishnan/downloads/
>> equilibrate_300K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> equilibrate_300K.namd>
>>>
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> equilibrate_300K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> equilibrate_300K.namd>>
>>> d) production @300K:
>>>
>> http://www.iab.keio.ac.jp/~krishnan/downloads/
>> production_300K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> production_300K.namd>
>>> <
>> http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> production_300K.namd>
>>> e) heating to 520K:
>>>
>> http://www.iab.keio.ac.jp/~krishnan/downloads/
>> heating_to_520K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> heating_to_520K.namd>
>>>
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> heating_to_520K.namd>
>>> f) equilibration @520K:
>>>
>> http://www.iab.keio.ac.jp/~krishnan/downloads/
>> equilibrate_520K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> equilibrate_520K.namd>
>>>
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> equilibrate_520K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> equilibrate_520K.namd>>
>>> g) production @520K:
>>>
>> http://www.iab.keio.ac.jp/~krishnan/downloads/
>> production_520K.namd
>> <http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> production_520K.namd>
>>> <
>> http://www.iab.keio.ac.jp/%7Ekrishnan/downloads/
>> production_520K.namd>
>>>
>>> I ran these under NPT.. so some of the comments in the files
>> might not
>>> make sense. (These were put in when I was initially doing an NVT
>>> ensemble).
>>>
>>> Do let me know if you see anything wrong.
>>>
>>> Thanks in advance.
>>>
>>> Cheers,
>>>
>>> Arun
>>>
>>> On 9/5/07, *Monika Sharma* < mon_sharma_at_research.iiit.ac.in
>> <mailto:mon_sharma_at_research.iiit.ac.in>
>>> <mailto:mon_sharma_at_research.iiit.ac.in
>> <mailto:mon_sharma_at_research.iiit.ac.in>>> wrote:
>>>
>>> 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.
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>>>>
>>>
>>
>>
>>
>
Neema Salimi
nsalimi_at_msg.ucsf.edu
University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143
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