AMBER Archive (2008)

Subject: Re: AMBER: restraint box dimension

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Fri Apr 11 2008 - 04:56:17 CDT

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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