AMBER Archive (2005)

Subject: Re: RE: AMBER: problem in minimization

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Thu Jun 02 2005 - 02:39:36 CDT

Dear Ross,
             Thanks for your information. i have checked the inpcrd
file. in which there are some atoms are not in the correct position.
once again,i will try to make the input file. moreover in my system each
molecule contains 102 atoms totally 64 molecules.

many thanks
Anand.S

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Wednesday, June 1, 2005 6:56 pm
Subject: RE: AMBER: problem in minimization

> Dear Anand,
>
> > i am trying to minimize the cluster struture of
> > organic molecules containing 64 molecules, but the energy minimizing
> > ended with the following error..could anyone inform the
> > reason for this
> > error..
>
> > Here is the input file:
> > min (no shake, periodic) - just enough to relax for md,
> > system:PIMB-monomer
> > &cntrl
> > imin = 1, igb = 0, maxcyc = 1000000,
> > ntc = 1, ntf = 1, ntb=0, nsnb = 999,
> > cut = 4.0, scee = 1.2,
> > &end
>
> A few comments here:
>
> 1) Maxcyc = 1000000 -> This is a very large number of minimisation
> steps to
> be running, do you intend to get to a very good minimum or are you
> justcleaning things up prior to MD? In the latter case maxcyc of
> 500 or so is
> plenty.
>
> 2) nsnb = 999 -> Is there a reason for changing this from the
> default of 25?
>
> 3) cut = 4.0 -> This way way way too short a cut off. For periodic
> boundaries the minimum should be 8.0A but for gas phase and
> implicit solvent
> it needs to be much bigger, say 16 angstroms or more. While this
> will make
> your simulation very slow it is essential to get reasonable
> results. You
> cannot hope to get meaningful results with a cutoff of only 4
> angstroms.Getting the wrong answer quickly is not a good idea.
>
> > | Flags: ISTAR2 MPI
>
> You don't state how big your system is but ISTAR2 limits you to
> 2^15 atoms =
> 32768.
> You may want to recompile with ISTAR4 if your system is larger than
> this.
> > | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic
> simulation> Ewald PARAMETER RANGE CHECKING:
> > parameter nfft1: (grid size) has value 432
> > This is outside the legal range
> > Lower limit: 6 Upper limit: 256
> > Check ew_legal.h
>
> This is suggesting that the virtual box that sander creates around
> yoursystem is 432-extraboxdim(60 anstroms) = 372 angstroms in the x
> direction.At this the y and z directions have not even been
> checked. Is your system
> really this big? It suggests to me that you have a problem in your
> inpcrdfile - perhaps you have an atom a long way away? Try creating
> a pdb from
> this inpcrd file and looking at it. Alternatively your inpcrd file
> may be
> corrupted in some way. Please check your input. If you really have
> a system
> this big and it is something really worth looking into then please
> get back
> to me and we will discuss options.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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