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 Thu Aug 04 2011 - 21:00:02 PDT
