Re: [AMBER] Amber and Short Bonds

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Tue, 27 Mar 2012 00:02:02 +0000

Yes.
These are the minimisation input files I use:
First minimisation: initial solvent + ions min
 &cntrl
  imin=1,
  maxcyc=1000,
  ncyc=500,
  ntpr=100,
  ntb=1,
  ntr=1,
  cut=8.0,
/

Second minimisation: full min
 &cntrl
  imin=1,
  maxcyc=2500,
  ncyc=1000,
  ntpr=100,
  ntb=1,
  ntr=0,
  cut=8.0,
 /

Both give errors during the minimisation, saying .... RESTARTED DUE TO LINMIN FAILURE ...
The first one reaches conclusion, but the second one has five such errors and crashes with ***** REPEATED LINMIN FAILURE *****
There still is restart file, but proceding with heating and density equilibration, the simulation just stops.
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Jason Swails [jason.swails.gmail.com]
Sent: 27 March 2012 00:47
To: AMBER Mailing List
Subject: Re: [AMBER] Amber and Short Bonds

But did you minimize first?

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Mar 26, 2012, at 7:18 PM, "Aronica, Pietro" <pietro.aronica07.imperial.ac.uk> wrote:
>> Also, make sure you haven't drastically increased the bond force
>> constants. The values used are right at the edge of stability.  The fact
>> that you have to go to shorter time steps suggests that you boosted the
>> force constants for some reason...
>
> Hello,
> no, the force constants are those of "normal" bonds, standard values of CT-CT and CT-HC. The only thing I've changed is the equilibrium bond length.
> ________________________________________
> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Thomas Cheatham [tec3.utah.edu]
> Sent: 26 March 2012 21:21
> To: jason.swails.gmail.com; AMBER Mailing List
> Subject: Re: [AMBER] Amber and Short Bonds
>
>> The equilibrium bond distances should have little effect on the
>> stability of your simulation, I would think.  You don't have to worry
>> about VDW and EEL clashes between bonded pairs (since those interactions
>> are excluded from bond/angle partners).
>
> Also, make sure you haven't drastically increased the bond force
> constants. The values used are right at the edge of stability.  The fact
> that you have to go to shorter time steps suggests that you boosted the
> force constants for some reason...
>
>
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Received on Mon Mar 26 2012 - 17:30:03 PDT