Hi,
Your plot doesn't make sense to me. Assuming your axis labels are
flipped (i.e. temperature is the Y axis), I don't see how your system
could jump from ~298 K to ~317K, then to ~330 K, then to ~325 K in
what looks like one frame each time. At any rate, I don't think the
AMD potential boost would affect your temperatures like this anyway
since the thermostat is constantly trying to keep your system at the
correct temperature. If there were an effect I would expect it to be a
gradual drift rather than a sudden jump. Could you send me off-list
the output file that you are getting your temperature data from so I
can take a closer look? Thanks.
-Dan
On Mon, Nov 4, 2013 at 12:41 AM, O Z <roza2006.hotmail.fr> wrote:
> Dear Amber users,
>
> I have been running Accelerated MD on my system. I set up my aMD parameters as explained on the Amber manual:
>
> from 10ns MD results (trajectory from 50 to 60 ns).
>
>
>
> ave Dihedral: 2095.80
>
>
> ave EPtot: -194481.05
>
>
> total atoms: 60616
>
>
> protein residues: 199 (3.5*199=696.5)
>
>
> AlphaD: 1/5 * 696.5 = 139.3
>
>
> EthreshD: 696.5 + 2095 = 2791.5
>
>
> alphaP: 60616 * (1/5) = 12123.2
>
>
> EthresP: -194481.05 + 12123.2 = -191091.1
>
> I used these parameters as follow:
>
> &cntrl
>
>
> imin=0,
>
>
> ntx=5,
>
>
>
>
>
> ntpr=25000, ntwx=25000, ntwe=25000, ntwprt=0,
>
>
>
>
>
> ntf=2, ntb=2, cut=12.0, ntp=1, pres0=1.0, comp=44.6, taup=1.0,
>
>
>
>
>
> iwrap=1, nscm=250,
>
>
>
>
>
> nstlim=25000000, dt=0.002,
>
>
>
>
>
> ntt=3, temp0=298.0, tautp=1.0, gamma_ln=3, ig=-1,
>
>
>
>
>
> ntc=2, irest=1,
>
>
>
>
>
> iamd=3,EthreshD=2791.5,
>
>
>
>
>
> alphaD=139.3,EthreshP=-191091.0549,
>
>
>
>
>
> alphaP=12123.2
>
>
>
>
>
> /
>
>
> I am running aMD at 298K but in the output file I noticed
> that the temperature raises a lot from 298K to about 320K (please see file attached).
>
>
> Is that due to the boost function? Or is it a normal behaviour, even if I use the NPT ensemble?
>
> Many thanks for your help.
> Regards.
> OZ
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Nov 04 2013 - 10:30:02 PST
