AMBER Archive (2006)

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

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Mon Feb 20 2006 - 14:32:13 CST

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
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu