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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Received on Fri Aug 05 2011 - 03:30:04 PDT
