Ok, as a new learner,I have got some useful things from these discussions . Thanks for your help !
At 2011-08-06 12:59:55,"Jason Swails" <jason.swails.gmail.com> wrote:
>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 - 23:00:03 PDT
