AMBER Archive (2008)

Subject: Re: AMBER: restraint box dimension

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Apr 11 2008 - 05:22:38 CDT

set ntpr=1 so you can see your initial restraint energy.
perhaps you made a mistake in changing xconst.

On Fri, Apr 11, 2008 at 5:56 AM, aneesh cna <aneeshcna_at_gmail.com> wrote:

> hai
> Thanks for your immediate reply. I tried to modify the xconst()
> subroutine in ene.f. (
> http://structbio.vanderbilt.edu/archives/amber-archive/2005/0623.php). I
> want to keep restraint on X and Y axis and allow the Z axis to move. But job
> got terminated by showing the message as follows
>
> ......................................................................................................................................
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE
> INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 3618004
> | TOTAL SIZE OF NONBOND LIST = 3618004
> vlimit exceeded for step 0; vmax = 37.3013
> vlimit exceeded for step 1; vmax = 192.7421
> vlimit exceeded for step 2; vmax = 56.9104
> SANDER BOMB in subroutine nonbond_list
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart sander
>
> .....................................................................................................................
> Here is my input...
>
> imin=0,ntx=7,irest=1,
> ntb=2,ntp=1,taup=0.2,pres0=1.0,
> nstlim=25000,dt=0.002,
> tempi=300.0,temp0=300.0,ntt=1,tautp=2.0,
> ntc=2,ntf=2,
> ntpr=100,ntwx=0,ntwe=0,
> cut=10.0,iwrap=1,ntr = 1,restraint_wt = 10.0,restraintmask = ':1-2873'
>
> ...................................................................................................................................
> Why this type errors coming? How can I solve this? Did I do any mistake
> while modify the code for keeping restraint on box dimensions? If yes.
>
>
>
>
> On Wed, Apr 9, 2008 at 6:04 AM, David A. Case <case_at_scripps.edu> wrote:
>
> > On Tue, Apr 08, 2008, aneesh cna wrote:
> >
> > > I am using 9.0 version of Amber.I would
> > like to
> > > know, whether there is a way to restraint box dimensions in two axis
> > and
> > > leave other free in Amber?
> >
> > Not without modifying the code itself.....dac
> >
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>
>

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