A minor clarification to what Carlos said: the only energy differences that
have any meaning are between different conformations of the same exact
system treated with exactly the same force field.
Comparing the energy of one conformation treated with ff03.r1 with another
treated with ff99SB is meaningless as well.
HTH,
Jason
On Fri, Aug 5, 2011 at 6:25 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> these values really have no meaning; only the energy difference
> between different conformations matter.
>
> seeing 1 simulation fold and another not is anecdotal- you would need
> to know if this difference is reproducible. it is perfectly acceptable
> to run 2 simulations of this length with the same force field and have
> 1 fold and the other not. always determine the precision
> (reproducibility) of your results before you make comparisons to
> results where you changed something.
>
> On Thu, Aug 4, 2011 at 11:58 PM, zhouhaibin2008.ok
> <zhouhaibin2008.ok.163.com> wrote:
> > Hi all,
> > Like amber tutorial B3, I wanted to simulate TC5b in linear state to see
> if it can reach the folded state . In this simulation , I used two different
> force fields , ff03.r1 and ff99SB, to built the linear states . When run
> sander , I used the same input file for the two simulations to optimise ,
> heat the system and run MD production . Here is the MD production input file
> :
> > &cntrl
> > imin = 0, irest = 1,
> > ntx = 7, ntb = 0,
> > ntr = 0, igb = 5,
> > cut = 999.9, rgbmax = 999.9, ntc = 2,
> > ntf = 2, ntt = 3,
> > gamma_ln = 4.0, tempi = 325.0,
> > temp0 = 325.0, nstlim = 5000000,
> > dt = 0.002, ntwr = 500,
> > ntpr = 500, ntwx = 500
> > /
> > When these simulations ended , I found the linear state using the ff03.r1
> force field reached the folded state , but the linear state using ff99SB not
> . However when I check the out file , I found the EPTOT using ff03.r1 was
> about -200, but the EPTOT using ff99SB was about -400.I don't known why the
> difference is so big , and I think the folded state should have a lower
> EPTOT, but the it does not.
> > Does the difference result from the different charges used by different
> force fields .
> >
> > Thank you in advance !
> >
> >
> >
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> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 05 2011 - 22:30:03 PDT
