AMBER Archive (2003)

Subject: Re: water box distortion

From: David A. Case (case_at_scripps.edu)
Date: Fri May 23 2003 - 18:13:40 CDT

On Fri, May 23, 2003, GUILLERMINA L ESTIU wrote:

> I am running simulations (amber 7) for a sistem of 2500 residuos (50000 after
> building the water box)
> I am trying to equilibrate the system. As a way of starting, I am heating only
> the solvent, but the water box is not kept "cubic"

You can use the "image" command in ptraj to map your atoms back to a unit
cell (no need to re-run the trajectory).

> molecular dynamics run
> &cntrl
> imin=0, irest=1,
> ntx=5, ntr=1,
> lastist=9000000,
> lastrst=12000000,
> tempi= 300.,
> ntt=1, temp0=300.0, tautp=0.5,
> ig=71277, heat=0.0,
> ntb=1, ntc=2, tol= 0.00001, ntf=2,
> scee=1.2, dt=0.0005,
             ^^^^^^^^^ this is too short, use something like 0.001

> cut=9.0, nsnb=25,
   ^^^^^^^ the default of 8.0 should be fine, and will save time
              nsnb is not necessary (but shouldn't hurt....)

> nstlim=100000,
   ^^^^^^^^^^^^^ this is pretty long for a single equlibration run; if
                  you are new to Amber, run shorter jobs and check the outputs

> vlimit= 20
> ntwe=50, ntwx=50, ntpr=10, ntwr=100,
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ these all seem very small for
                             equilibration; be sure you have lots of disk
                             space if you plan to save such a big system
                             every 25 fs!

> &end
> Group input for restrained atoms
> 10000.0
   ^^^^^^^ this is way to big! Try a value of 10. instead
> RES 1 2479
> END
> END
>

..good luck....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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