it depends on the system size and as Adrian Roitberg said, it can
be larger with a short cutoff on nonbonded interactions.
for a small system 20-30deg would not surprise me.
On 7/20/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
> Sir,
> i have started the normal MD for that temperature for same time to compare
> the results.
> But from my previous mail i mean that is it normal to have (20-30 degree)
> fluctuations in temperature even though system is attached to langevin
> thermostat with implicit solvent.
> Regards
> Priya
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> I don't understand what you mean by this- you did the comparison
> and they do match or do not match??
>
> On 7/20/07, priya priya wrote:
> >
> > Sir,
> > so fluctuations are normal in MD and REMD using thermostat.
> > Regards
> > Priya
> >
> > Carlos Simmerling 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
> > > >
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Received on Sun Jul 22 2007 - 06:07:47 PDT
