[gmx-users] Both Steepest and Conjugate didn't converge

[Pradip Kumar Biswas]

Hi David,

I was trying to communicate the files necessary to reproduce what I got  
but failed
due to its size (872 KB). The system is a tetrahydrobiopterin solvated  
in tip3p water.
We took care of -DFLEXIBLE as mentioned by Tim Hohm (It was a problem  
before
we notice it and then Fmax was quite bigger). I am sending here tails  
of two outputfiles
and I can send he parameter file directly to you if you do not find any  
apparent
error from what we are doing and want to run a test.

Ps. Unfortunately I am yet to locate the file where I ended up with  
Fmax=~10^4.

For ns_type=grid:
------------------------------------------------------------------------ 
------------------------------------
Step 359, Epot=-3.452539e+04, Fnorm=5.386e-01, Fmax=2.420e+01 (atom 11)

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 0.0001

writing lowest energy coordinates.

Back Off! I just backed up BH4_gmxopt_b4pr.gro to  
./#BH4_gmxopt_b4pr.gro.2#

Low-Memory BFGS Minimizer converged to machine precision in 360 steps,
but did not reach the requested Fmax < 0.0001.
Potential Energy  = -3.45253896257264e+04
Maximum force     =  2.42033918696309e+01 on atom 11
Norm of force     =  5.38638872105523e-01

gcq#40: "Yeah, a Wuzz, Or a Jerk" (F. Black)
------------------------------------------------------------------------ 
-------------------------------------

With ns_type=simple:
------------------------------------------------------------------------ 
-------------------------------------
Step 1663, Epot=-3.453336e+04, Fnorm=6.344e-06, Fmax=1.787e-04 (atom 10)

Step 1664, Epot=-3.453336e+04, Fnorm=4.539e-06, Fmax=7.339e-05 (atom 30)

writing lowest energy coordinates.

Back Off! I just backed up BH4_gmxopt_b4pr.gro to  
./#BH4_gmxopt_b4pr.gro.1#

Low-Memory BFGS Minimizer converged to Fmax < 0.0001 in 1664 steps
Potential Energy  = -3.45333644934845e+04
Maximum force     =  7.33891581076472e-05 on atom 30
Norm of force     =  4.53925827182244e-06

gcq#255: "Drugs are Bad, mmokay" (South Park)



Pradip.


On Feb 9, 2006, at 2:48 AM, David van der Spoel wrote:

> Pradip Kumar Biswas wrote:
>> Hi Prettina,
>> I saw the reply of Tsjerk but I want to add that if we use 'simple'  
>> neighbor search
>> (ns_type = simple) instead of 'grid', I always get pretty good lower  
>> energy for e.m.
>> And once we use ns-type=grid, most of the time we encounter the  
>> message
>> you got. Could you try your energy minimization with ns_type=simple?
> If you can show me a system where this happens then I would be  
> interested in seeing it. These should be identical.
>
>
> -- 
> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
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