AMBER Archive (2003)

Subject: RE:RE: TAUP and density problem

From: yuan bo (yuanbous_at_yahoo.com)
Date: Mon Feb 17 2003 - 03:50:08 CST

--- case <case_at_scripps.edu> wrote:
> >===== Original Message From yuan bo
> <yuanbous_at_yahoo.com> =====
>
> >I also simulate one protein in nonaqueous solvent.
>
> Which non-aqueous solvent? What is the density
> supposed to be?

solvent is actonitrile and it's density should be
0.7822g/cm3 in experiment.
I want to know how density is calculated in sander
simulation. Is the solute included in density
calculation? From my results, the density seems to
include solute(protein),right? If so, the density
caculated in MD should not be equal to the actual
density. larger or smaller than actual density?
>
>
> >
> >&cntrl
> >imin=0,ntb=2, ntp=1, cut=12.0, ntwx=200, ntwe=200,
> >nstlim=100000, ntc=2, dt=0.001, ntt=1, ntx=5,
> > irest=1, ntpr=200,ntf=2,taup=2.0( or 1.0)
> >&end
> >
> The only thing I can see is that you probably should
> be using ntx=7 (not
> 5) if the previous runs were with constant P.
> Otherwise, you will be
> starting over with you initial volume and density,
> rather than the one
> from the end of the previous run.
>

I check my output file. As NTX=7, NTX=5 also start
over with box size and density of previous run, not
initial volume and density.
My NPT equilibration are done based on the following
step
(1)150 ps NPT with NTC=3 and NTF=3 and taup=0.2,other
parameters are same as the input file above. the
reason why set NTC=3 and taup=0.2 is that I find the
density converge relatively quick in previous exercise
(although the amount of solvent is smaller, buffer is
8.0 in solvatebox before) The density gradually rise
up to 0.74.
(2) Then 200ps NPT simulation is done based on
previous 150ps calculation: NTC and NTF swith to 2 and
taup is set to 2.0. As mentioned in last email, the
simulation would results in ewald bomd if taup is set
less than 1.0 together with NTC=2. The density drop
from 0.74 to about 0.68 within first about 20ps and
then start to gradually increase to 0.72 in last 180ps
simulation.
(3) Then additional 200ps NPT MD is done with NTC and
NTF=2 and taup=1.0 and other options are same as input
file above. Because I find that taup=2.0 make density
increase too slowly compared to actual density
0.7822,I switch taup=2.0 to 1.0. The density increase
from 0.72 to 0.85 within 100ps and then drop from 0.85
to 0.79 with last 100 ps. But it seems that the trend
of density will drop in future. ( I will do additional
100ps NPT to check if the density would converge.) So
the density seems not to meet equilibration.
  The tempature vary very small in simulation and
enery is not stable.
Did Anybody ever do MD in organic solvent before?
Could you give me some experiences and
suggestions,especially about TAUP value? Would
different TAUP value lead to different final density?
Why do my density still not meet the equilibration
after 550ps? My system have 3300 acetonitrile
molecules
Thanks in advance.
yb

>
> ...good luck...dac
>
>
==================================================================
> David A. Case | e-mail:
> case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax:
> +1-858-784-8896
> The Scripps Research Institute | phone:
> +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
>
> La Jolla CA 92037 USA |
> http://www.scripps.edu/case
>
==================================================================
>
>

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