Re: offset of temperature when running MD with CAP and no periodic conditions

From: Andreas Svrcek-Seiler <svrci_at_tbi.univie.ac.at>
Date: Thu 19 Sep 2002 19:11:31 +0200 (CEST)

Hi,
> imin=0, ntx=5, ntpr=500,ntwx=500,
> ntwe=500, ntcm=1, igb=2, dielc=1,
> cut = 14.0, nscm = 1,
      ^^^^^^^^^^
...You are using a hard cutoff for the Coulomb interaction,
this might be the source of all kinds of weird behavior.
> EELEC = 4195.5463 EHBOND = .0000 CONSTRAINT =
... the large fluctions of EELEC also seem to point to the cutoff (I
believe, experts correct me please :-).

I'd set the cutoff to a value larger than the largest diameter of your
system, nsnb to some large number (the pairlist doesn't need to be
updated in this case) and look what happens then.


hope it helps,
regards
Andreas 





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From prbj_at_rediffmail.com 19 Sep 2002 17:27:48 -0000
Message-id: <20020919172748.28815.qmail.webmail26.rediffmail.com>
Date: 19 Sep 2002 17:27:48 -0000
From: Prem  Raj <prbj_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: compiling without ISTAR2
In-Reply-to: <3D89F0D8.BE7268BE.ibpc.fr>
Dear Amber users,
          I started a dynamics simulation on a protein molecule 
with
explicit water using Amber 6 ( sander_classic). The system has a 
total of
34800 atoms. when I ran the initail minimisation I got the below 
error.
           GROUP    8 HAS HARMONIC CONSTRAINTS   500.00000
  GRP    8 RES  141 TO   157
       Number of atoms in this group  =   288
     ----- END OF GROUP READ -----
Ligand Grid: OFF (not requested)
    Too many atoms for 16 bit pairlist -
      Recompile without ISTAR2
In which file should I make these changes before I recompile the 
software.
************************************************************
  Prem Raj B. Joseph
  Dept. of Chemistry and Biochemistry
  Howard Hughes Medical Institute
  University of Maryland Baltimore County
  1000 Hilltop Circle, Baltimore, MD 21250
  Ph: (410)455-2718
  email: prbj123_at_rediffmail.com
Residence:
  4747 Drayton Grn
  Baltimore, MD - 21227
  Ph(Res): (410)247-2413
*************************************************************
thanks in advance.
Received on Thu Sep 19 2002 - 10:11:31 PDT
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