[gmx-users] Energy minimizations with gmx3.2

[Kay Gottschalk]

I had the same problem. For me it worked miraculously to increase the  
step size to dt = 0.01. Then it converged. Don't ask me why...
Cheers,
Kay

On May 17, 2004, at 4:51 PM, Marc Vogt wrote:

> No I had not been able to find any solutions in the archive, but I  
> tried
> just now and although the minimization ran for 252 steps in 3.2.1
> with define = -DFLEXIBLE instead of 37 steps for define = -DFLEX_SPC,
> it still failed.:
>
> With 3.2.1 and define = -DFLEXIBLE and contraints=none
> --------------------------------------------------------------
> Step=  251, Dmax= 1.7e-06 nm, Epot= -1.79236e+05 Fmax= 2.01564e+03,  
> atom= 68
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
> Double precision normally gives you higher accuracy.
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up test.gro to ./#test.gro.2#
>
> Steepest Descents converged to machine precision in 252 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.7923609e+05
> Maximum force     =  2.0180422e+03 on atom 68
> Norm of force     =  9.6549727e+03
>
>
> With 3.1.4 and define=DFLEX_SPC
> -----------------------------------------------------------------
> Step=  109, Dmax= 6.4e-03 nm, Epot= -1.75318e+05 Fmax= 9.59784e+02,  
> atom= 6814
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up mintraj.trr to ./#mintraj.trr.2#
>
> Back Off! I just backed up test.gro to ./#test.gro.3#
>
> Steepest Descents converged to 1000 in 110 steps
>   Potential Energy  = -1.75318e+05
> Maximum force:  9.59784e+02
>
>
>
>
> -----------------------------------------------------------------
> -----------------------------------------------------------------
>
> Other than the define= field, the mdp is the same
>
> title               =  testww
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  1000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> epsilon_r           =  1
>
>
> thanks,
> Marc
>
>
>>
>> On Mon, 2004-05-17 at 15:05, Marc Vogt wrote:
>>> I had the same problem using DFLEX_SPC.  Never could resolve it
>>> along with a restart problem.  Both in 3.2.1.
>>> Consequently, I'm still using 3.1.4.
>> Have you tried
>> define = -DFLEXIBLE
>> constraints = none
>>>
>>> Marc
>>>
>>>>
>>>> Which water model you use?
>>>> I encountered the same problem when using TIP4P.
>>>>
>>>> Tanos wrote:
>>>>
>>>>>    Hi folks,
>>>>>    Since I started to use gmx 3.2 my energy minimizations stopped  
>>>>> to
>>>>> converge to emtol. All of them have converged to the machine  
>>>>> precision
>>>>> !!!!!! Is that happening to someone else ??? If ss, does someone  
>>>>> knows
>>>>> the reason ?????
>>>>>    Thanks in advance.
>>>>>    Tanos C. C. Franca - IME
>>>>>    Rio de Janeiro - RJ
>>>>>    Brazil
>>>>>
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>>>>
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>> --  
>> David.
>> ______________________________________________________________________ 
>> __
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone:  +46 18 471 4205  fax: +46 18 511 755
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>
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Rehovot
Israel