Sir,
so fluctuations are normal in MD and REMD using thermostat.
Regards
Priya
Carlos Simmerling <carlos.simmerling.gmail.com> wrote: have you plotted the temperature histogram for the REMD
run and compared to long MD at the same temperature?
make sure you are comparing statistical analysis and not
just looking at a few numbers. also don't just look at low
T, make sure you are comparing to MD at the same thermostats
as your REMD.
On 7/20/07, priya priya
wrote:
> Dear Sir,
> In normal MD there is not too much fluctuation in temperature specified that
> is +10 from the temp0. but here more than 30degree fluctuations are seen,
> and if i draw the specific heat graph from the potential energy and
> temperature it is a flat curve without any peak.
> From my procedure is there any mistake u an observe.
> Thanks,
> Regards
> priya
>
> Carlos Simmerling wrote:
> is this different from what you see in normal MD for
> this system using this thermostat and temp0?
> in other words, is this expected behavior for REMD, or
> do REMD and MD differ?
>
> On 7/20/07, priya priya wrote:
> > Dear All,
> >
> > I am doing replica exchange method using implicit solvent, looking into
> the
> > results summary.TEMP created by using reminfo file i found that the
> > temperature is fluctuating a lot even though i am using langevin
> > thermostat.I started from temp range 273K to 373K but in the output file
> > there are temperature 402 K and above also.
> > Method i followed is as under with the input files:
> > 1) minimized the linear structure generated by Xleap: input file:
> > Stage 1 - minimisation of am15-42 in implicit solvent
> > &cntrl
> > imin=1, maxcyc=5000, ncyc=2500,
> > cut=999., rgbmax=999.,igb=1, ntb=0,
> > ntpr=100
> > /
> >
> > 2) heated the system for different temperatures which could act as the
> > starting conformations for the Replica exchange method. input file was
> (only
> > temp different in files):
> > am15: 100ps MD in implicit solvent
> > &cntrl
> > imin = 0,
> > ntb = 0, igb = 1,
> > cut = 10,
> > tempi = 373.715, temp0 = 373.715,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 50000, dt = 0.002,
> > ntpr = 50, ntwx = 50, ntwr = 50
> > /
> > 3) REMD using the reference rst from from the previous step at different
> > temp
> > input file (different temp for different replicas):
> > &cntrl
> > imin = 0, nstlim = 100, dt = 0.002,
> > ntx = 5, tempi = 360.893,temp0 =360.893,
> > ntt = 3, tol = 0.0000001,
> > ntc = 2, ntf = 1, ntb =0,
> > ntwx = 5, ntwe = 0, ntwr = 5, ntpr = 5,
> > cut =10.0, scee = 1.2, ibelly =0,
> > ntr = 0, gamma_ln = 1.0,offset = 0.09
> > nscm = 500, igb = 1,
> > irest = 1,numexchg = 50000, repcrd = 0,ntave = 0,
> > /
> >
> > System is running fine with showing exchanges in the log file that has
> been
> > created, but if i extract output for the various repinfo file created for
> > different replicas, i found strange fluctuation in temp which are not the
> > range given.
> > Will anybody see error in my steps and my input file.
> > Suggestion are welcomed.
> >
> > Regards
> >
> >
> > ________________________________
> > Unlimited freedom, unlimited storage. Get it now
> >
> >
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Received on Sun Jul 22 2007 - 06:07:45 PDT
