Dear Sir
nsnb option is to determine the frequency of nonbonded list updates when igb=0 (manual page 101 amber9), and in my simulation igb=1.
i have changed ntwx=100.
But too much fluctuations can be seen in explicit solvent but not in implicit solvent.
If i draw the specific heat graph vs temp ;calculated from the potential energy and temperature it is a flat curve without any peak.
>>From my procedure is there any mistake u an observe.
Regards
Priya
Adrian Roitberg <roitberg.qtp.ufl.edu> wrote: Priya,
I believe your value of cut might be a bit small and then you can get
strange fluctuations.
Can you try a quick run using a larger value of cut ?
Maybe 15 or 16 ?
Also, what is the value of your nsnb in the output file ?
Maybe set that to 10 or so.
On another note:
nstlim=100 is a very fast exchange rate, which we actually prefer, but
in amber 9, specially writing as often as you do (ntwx=5) will make your
runs go very slowly.
Cheers
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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>>
>>
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Received on Sun Jul 22 2007 - 06:07:45 PDT
