Dear dac,
On Fri, Mar 6, 2009 at 8:27 PM, David A. Case <case.biomaps.rutgers.edu> wrote:
> On Fri, Mar 06, 2009, BERGY wrote:
>
>>
>> I am doing a Simulation of ADNA (12mer) for 10ns using AMBER9. On
>> analyzing, i find that the RMSD goes well above 20-30 Angstroms. And
>> visualization I see that 3 of the Bases got flipped out from the
>> middle of the helix and the helix looks very much straightened like
>> a ladder.
>
> Presumably, everything up to the "production" step was fine, since you
> had strong restraints to the starting structures. But you should check
> this.
>
>> --------------production---10ns---in 10ps steps
>> ADNA-md1 12mer solvent-+ randomized ions
>> &cntrl
>> imin = 0, irest = 1, ntx = 7,
>> ntb = 2, pres0 = 1.0, ntp = 1,
>> taup = 2.0,
>> cut = 10,
>> ntc = 2, ntf = 2,
>> tempi = 300.0, temp0 = 300.0,
>> ntt = 3, gamma_ln = 1.0,
>> nstlim = 5000, dt = 0.002,iwrap=1
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>
> First, check to see *when* the DNA fell apart -- was it in the first 10
> ps? You may have a bad structure or bad contacts. Then jumping
> directly from very strong constraints (force constant of 25) to none
> could cause bad behavior right away.
>
> Alternatively, you are hitting the random number problem with ntt=3: you
> are running many very short runs, then restarting with the same random
> number seed over and over again. This could really explain the behavior
> you see, if nothing else is wrong. You *must* use a new value of ig at
> each restart...see the mailing archives for a discussion of this point.
> (It's not clear why you are running 1000 separate short simulations
> anyway.)
Sir i have made corrections and made runs of 200ps each now. thank you
for the help. Also I read the archive mailing list. And I came to
know that we should use ig=-1 option to get random seed that will use
the wallclock time. DOES it apply to AMBER 8/9 too.
http://archive.ambermd.org/200811/0254.html
these were the lines that was posted in the mailing archive by ROSS on
.....Date: Sat Nov 22 2008 - 09:18:57 PST.."The main point to take
home here is that you should probably 'ALWAYS' be changing the random
number seed (ig=) whenever you restart a simulation - in fact you
should probably never run any two MD runs with the same seed (except
for testing / debugging). A simple solution to this (in AMBER 10) is
to set ig=-1 and then it will use the wallclock time in microseconds
to seed the random number generator.".....................
>
> ...hope this helps...dac
>
>
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Received on Fri Mar 13 2009 - 01:33:01 PDT
