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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 15 2012 - 07:30:04 PDT
