# Re: equilibrating water in sander

From: Yong Duan <yduan_at_chem.udel.edu>
Date: Thu 21 Jun 2001 00:27:02 -0400

At present, sander does not support non-isotropic pressure scaling (i.e.,
NTP=2 is not supported). If your system is a box of water, isotropic
pressure scaling should be used since only isotropic pressure makes
physical sense in water (i.e., pressure of sea water depends on the depth
of water, not the orientation of your probe).

Hope this helps.

yong

On Wed, 20 Jun 2001, Elizabeth K. White wrote:

> When I follow the excellent tutorial (Example 2, a more complicated
> protein example), the sander run for constant P fails. It seems that
> ntb=2 and ntp=2 are mutually incompatible:
>
> NTP ( 2) must NOT be 2.
>
> Non-isotropic scaling is currently NOT supported.
>
> Use NTP of 0 or 1
>
> *** input error(s)
>
> Is this really true, or have I made a mistake? Can anyone suggest a nice
> workaround? Can I get away with isotropic scaling if I make a cubic water
> box?
>
> Here is the input file:
> Constant pressure simulation
> &cntrl
> imin=0,
> nmropt=1,
> ntx=7, irest=1,
> scee=1.2, cut=9.0,
> ntt=1, tempi=300.0, temp0=300.0,
> ntb=2, ntp=2,
> ntc=2, tol=0.000001,
> ntpr=100, ntwr=99999,
> ntcm=1, nscm=1000, ndfmin=-3,
> ntr=1,
> nstlim=20000,
> &end
> &wt type='REST', istep1=0, istep2=1000, value1=1.0, value2=1.0, &end
> &wt type='END', &end
> LISTOUT=POUT
> DISANG=RST
> Group input for restrained atoms
> 5.0
> RES 1 99
> END
> END
>
> Thanks, Elizabeth White
>
Received on Wed Jun 20 2001 - 21:27:02 PDT
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