AMBER Archive (2009)

Subject: Re: [AMBER] High RMSD for DNA: A to B transition study

From: SENTHIL KUMAR (nucleic81_at_gmail.com)
Date: Fri Mar 13 2009 - 01:36:43 CDT

Dear dac,
On Fri, Mar 6, 2009 at 8:27 PM, David A. Case <case_at_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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber