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 Fri Jun 15 2012 - 23:00:02 PDT
