I agree with you of course, but if it truly does not unfold at high T
in normal MD, but does in REMD, this would suggest a bug. This is
unlikely, though...
On Thu, Jun 14, 2012 at 9:36 PM, Daniel Sindhikara <sindhikara.gmail.com> wrote:
> He said that there is loss in secondary structure and domains are moving
> apart which indicates unfolding.
> This isn't a bug, just too high of a temperature.
>
>
> On Fri, Jun 15, 2012 at 3:11 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> can you explain more about where you found that it is stable in MD but
>> not in REMD< using the same temperatures? this suggests a disturbing
>> bug.
>>
>> On Mon, Jun 11, 2012 at 2:15 AM, Soumya Lipsa Rath
>> <soumyalipsabt.gmail.com> wrote:
>> > I am working with Cyclin Dependent Kinases, using ff99sb forcefield.
>> > Simulation is run in implicit solvent, using igb=5. After raising the
>> > temperature to 300K, the protein is subjected to multisander
>> equilibration
>> > using procedure similar to that in the tutorial. I don't want to study
>> the
>> > unfolding of protein but a specific loop movement which I assume is
>> > restricted due to some energy barrier in normal MD simulation.
>> >
>> > Thanks
>> >
>> > On Sun, Jun 10, 2012 at 10:18 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> >
>> >> You need to give more detail like what your protein is, which force
>> field
>> >> you are using etc ... Do you know its melting temperature? Be specific
>> as
>> >> possible.
>> >> Hai Nguyen
>> >>
>> >> On Thu, Jun 7, 2012 at 11:58 PM, Soumya Lipsa Rath
>> >> <soumyalipsabt.gmail.com>wrote:
>> >>
>> >> > Dear Amber Users,
>> >> >
>> >> > I am trying to run Replica exchange MD simulation implicitly. During
>> the
>> >> > equilibration step and at higher temperatures, the structure of my
>> >> protein
>> >> > becomes distorted. I have given the chirality restraints on the
>> protein
>> >> > backbone. I wanted to know whether structural distortions at higher
>> >> > temperatures in normal or do I need to modify/add some parameters?
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Soumya
>> >> > _______________________________________________
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>
>
>
> --
> Dr. Daniel J. Sindhikara <http://goo.gl/fLAqx>
> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/> - Biwako Kusatsu
> Campus <http://www.ritsumei.ac.jp/eng/html/about/abo_08.html/#kusatsu>
> sindhikara.gmail.com
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Received on Fri Jun 15 2012 - 04:00:03 PDT
