AMBER Archive (2006)

Subject: Re: AMBER: Error in RST files in long simulations!

From: lucas luquitas (
Date: Mon Feb 20 2006 - 17:08:38 CST

Ok, thanks Carlos!
I checked it, if I understood well the idea to solve this is to wrap
the waters, setting iwrap=1, be sure to have nscm=xxstep. I prefered
to wrap my system when I analyse
my simulations as I never had this problem.
What I could not find is there is any posibility of restarting the
run, I can imagine
using the velocity information writing the rst coordinates using ptraj
or rdparm?

Regarding the image problem, here is my simple ptraj script:

trajin .protein1crd
trajout protein2.crd
rms first out rms @CA,C,N
center :1-33
strip :WAT


On 2/20/06, Carlos Simmerling <> wrote:
> search for restart and iwrap on the amber web page search bar (search
> mail list).
> the results of image/center/strip depends on what you ask ptraj to
> do. Since you didn't tell us that it's hard to help. Check the archives,
> this has been discussed before.
> lucas luquitas wrote:
> >Hi all,
> > I am ruuning a normal constant temperature simulation of small protein(34aa) in
> >a periodic box of TIP3P waters. The simulation is quite long around
> >80ns, the problem
> >is when I want to restart the simulation, my restart file is corrupted!!
> >When I check, I see that some of the coordinates are above 1000, so it
> >prints ***********.
> >The other thing is that when I image and center and strip to view the
> >traj with VMD, I see jumping in the coordinates, like if it were
> >moving between boxes!
> >
> > Here is the inp file:
> >&cntrl
> > imin=0,
> > ntc=2, ntf=2,
> > cut=12.0,
> > ntpr=500, ntwx=10000, ntwv=10000,ntwe=500,
> > nstlim=90000000, dt=0.002,
> > ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
> > ntx=5, irest=1, ntb=2,
> > ntp=1, PRES0=1, TAUP=1,
> > nscm=10000,
> > ntr=0,
> >&end
> >
> >
> >
> >Lucas
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