AMBER Archive (2005)

Subject: Re: AMBER: Minimization of avg structure-SANDER Bomb

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Thu Mar 17 2005 - 12:45:01 CST

Dear Prof. Case:

I tried with constant volume:

Input>>
Total minimization
&cntrl
ntx = 1, ntrx = 1,
ntpr = 50,
ntf = 1, ntb = 1, dielc = 1,
cut = 8.0, nsnb = 25,
scnb = 2.0, scee = 1.2,
ntr = 0,
imin = 1, maxcyc =15000, ncyc = 2500,
ntmin = 1, dx0 = 0.1, drms = 0.01,
temp0 = 300.0, tempi = 300.0, ntt = 0,
vlimit = 20.0,
npscal = 1, ntc = 1,
&end
&ewald
a=66.778, b=78.941, c=90.444,
alpha=90, beta=90, gamma=90,
order=4, verbose=0, netfrc=1,
ew_type=0, dsum_tol=0.000001,
vdwmeth=1,skinnb=1, nbflag=1,use_pme=1, eedmeth=1,
&end
------------------------------------
But the problem remains, it crashes immediately as before:

   4. RESULTS
--------------------------------------------------------------------------------

---------------------------------------------------
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 = 0.8987E-11 at 2.875760
---------------------------------------------------

* NB pairs 394 11607260 exceeds capacity ( 11607624) 0
     SIZE OF NONBOND LIST = 11607624
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.f
--------------------------------------------------------------------
I was trying with NPT because the simulation lasted in an NPT, and so I
averaged the structure from the last 200 ps of a 1.2ns trajectory, its this
average structure which is being used........

Thanks,
Vineet

From: "David A. Case" <case_at_scripps.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Minimization of avg structure-SANDER Bomb
>Date: Thu, 17 Mar 2005 08:51:59 -0800
>
>On Thu, Mar 17, 2005, Vineet Pande wrote:
> >
> > * NB pairs 394 11607260 exceeds capacity ( 11607624) 0
> > SIZE OF NONBOND LIST = 11607624
> > SANDER BOMB in subroutine nonbond_list
>
> > MY INPUT IS:
> > Total minimization
> > &cntrl
> > ntf = 1, ntb = 2, dielc = 1,
> > cut = 8.0, nsnb = 25,
> > imin = 1, maxcyc =15000, ncyc = 2500,
> > ntmin = 1, dx0 = 0.1, drms = 0.01,
> > ntp = 1, npscal = 1, ntc = 1,
> > &end
>
>Minimization doesn't know anything about constant pressure, but that
>*might*
>be messing up an internal size calculation. See if running this a constant
>volume will help. This is just a guess, but it seems worth a try, since
>we have certainly never tested the combination ntp=1 and imin=1. Does the
>error happen right at the beginning, or after some number of steps of
>minimization? (Set ntpr=1 to see more details of what is going on.)
>
>...good luck....dac
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

_________________________________________________________________
Don't just search. Find. Check out the new MSN Search!
http://search.msn.com/

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