Thanks for the suggestion. I'll try to run using your advice.
Soumya
On Sat, Jun 16, 2012 at 4:33 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 05:30:02 PDT
