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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Received on Thu Jun 14 2012 - 11:30:03 PDT
