you need to run at the same temperature as the REMD.
I think the bottom line here is that we are all telling you that you
can't run your system at 500K (either MD or REMD) without it
unfolding. the protein structure simply isn't stable at those
temperatures. A short run in exp;licit solvent may appear stable due
to viscosity slowing the unfolding, but it still too hot for your
protein. You need to find another way to study this problem besides
using high temperature, or you need to find a way (restraints) to keep
the structure stable and only allow part of it to move in REMD.
On Sat, Jun 16, 2012 at 1:33 AM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com> wrote:
> Sir,
>
> I ran MD in implicit solvent at 300K, it is showing stable secondary
> structure.
>
> Thanks,
> Soumya
>
> On Fri, Jun 15, 2012 at 8:39 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> you can't compare results with REMD in implicit solvent to MD in
>> explicit solvent. Run MD in implicit solvetn and see what happens. if
>> the structure is unstable, you should not move on to REMD. this is
>> true for any study of this type but especially so with igb=7, in my
>> experience it tends to lead to unstable secondary structure.
>>
>> On Fri, Jun 15, 2012 at 10:08 AM, Soumya Lipsa Rath
>> <soumyalipsabt.gmail.com> wrote:
>> > Sirs,
>> >
>> > I haven't been able to run REMD till now properly, I see the structural
>> > changes during equilibration step itself. For normal MD, in explicit
>> > solvent I had raised the temperature from 300K to 400K then run MD for
>> 5ns
>> > then again raised temperature from 400K to 500K and ran MD for another
>> 5ns.
>> > And as I had already mentioned not much change happened to most of the
>> > parts of my protein which has around 600 residues.
>> > So to overcome the barrier, I opted for REMD. As Daniel Sir had
>> suggested,
>> > I might be using a very high temperature, for which my protein gets
>> > unfolded,
>> > Presently, I am trying to run REMD using the temperature range of 300 to
>> > 400K. I have raised the temperature using normal equilibration to 300K, I
>> > bypassed the multisander equilibration steps as mentioned in the tutorial
>> > and I tried running REMD directly my remd.mdin file is as follows:
>> >
>> > Equilibration
>> > &cntrl
>> > irest=1, ntx=7,
>> > nstlim=500, dt=0.0002,
>> > irest=0, ntt=3, gamma_ln=1.0,
>> > tempi=300, temp0=XXXXX, ig=RANDOM_NUMBER,
>> > ntc=2, ntf=2, nscm=1000,
>> > ntb=0, igb=7,
>> > cut=999.0, rgbmax=999.0,
>> > ntpr=100, ntwx=1000, ntwr=100000,
>> > nmropt=1,
>> > numexchg=10,
>> > /
>> > &wt TYPE='END'
>> > /
>> > DISANG=chir.dat
>> >
>> > I have reduced the time step to avoid vlimit error. But when I check the
>> > temperature after the 2nd and 3rd step, it keeps on increasing to
>> > abnormally high values (i.e. 6000K!!) [when I try normal implicit MD and
>> > not REMD, it is running fine]
>> >
>> > Is it because I have by-passed the equilibration step or because I am
>> > running it in implicit solvent? I also don't get vlimit error in normal
>> MD,
>> > but I get this during REMD. Kindly help me get through this.
>> >
>> > Thanks,
>> >
>> > Soumya
>> >
>> >
>> > On Fri, Jun 15, 2012 at 6:59 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> >> Hi,
>> >>
>> >> On Thu, Jun 14, 2012 at 11:33 PM, Soumya Lipsa Rath
>> >> <soumyalipsabt.gmail.com> wrote:
>> >> > 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.
>> >> >
>> >> > During the MD run (in explicit solvent) I did not see any loss of
>> >> > secondary structure..
>> >>
>> >> Just to clarify, in your original post you wrote that you saw your
>> >> protein begin to unfold (loss of secondary structure etc) using REMD
>> >> with implicit solvent. You are comparing this to a previous normal MD
>> >> run in explicit solvent at high temperature, where you did not see any
>> >> loss of secondary structure.
>> >>
>> >> The problem here is that you are comparing two very different
>> >> timescales. You don't say how long you ran either of the simulations,
>> >> but in your REMD simulation you are first enhancing sampling with
>> >> replica exchange, then further enhancing sampling by using implicit
>> >> solvent (you don't say what thermostat you use and whether you employ
>> >> an NP term, which will also affect sampling). In contrast, you would
>> >> have to run the same system using normal MD with explicit solvent way
>> >> way way longer to see the same behavior. Unless you are convinced that
>> >> both the REMD and MD simulations are even somewhat converged I don'
>> >> think you should directly compare them.
>> >>
>> >> -Dan
>> >>
>> >> --
>> >> -------------------------
>> >> Daniel R. Roe, PhD
>> >> Lab Specialist
>> >> Department of Medicinal Chemistry
>> >> University of Utah
>> >> 30 South 2000 East, Room 201
>> >> Salt Lake City, UT 84112-5820
>> >> http://home.chpc.utah.edu/~cheatham/
>> >> (801) 587-9652
>> >> (801) 585-9119 (Fax)
>> >>
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Received on Sat Jun 16 2012 - 04:30:03 PDT
