I would most certainly CHANGE the values of ntc and ntf to compute all
forces for the minimization. Put them back to normal after minimization.
Also, see if you can create a system WITHOUT solvent and ions and see if
it also dies. It is important to separate solvent issues from internal
ones when diagnosing.
Third, look at the manual for the xmin minimizer. It is much more
efficient than the regular minimizers.
Adrian
On 3/26/12 5:02 PM, Aronica, Pietro wrote:
> 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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>>
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Mon Mar 26 2012 - 17:30:03 PDT
