[gmx-users] Re:Re: Re: Re:double precision minimization with version 3.3

[Yechun Xu]

>Message: 1
>Date: Tue, 21 Mar 2006 18:44:25 +0100
>From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
>Subject: Re: [gmx-users] Re: Re:double precision minimization with
>	version 3.3
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <200603211844.26211.Florian.Haberl at chemie.uni-erlangen.de>
>Content-Type: text/plain;  charset="utf-8"
>
>Hi,
>
>On Tuesday 21 March 2006 18:11, Yechun Xu wrote:
>> Dear gmx users,
>>
>>    First, I'd like to thank David's suggestion. It is not a bug of the
>> program but a problem of installation. Now it is fixed and works fine.
>>
>>    I met another problem about the double precision minimization (used for
>> NMA later) with l-bfgs in version 3.3. It seems the optimization will never
>> finish. The protein only includes 604 atoms (in vacuum) and the
>> optimization started almost three weeks ago but only reach something like:
>> "Step 29403607, Epot=-3.927499e+03, Fnorm=2.169e-01, Fmax=1.699e+00 (atom
>> 451)"
>>
>> So my question is that the l-bfgs optimization does take very long time or
>> there is some problem with my mdps file? Any suggestions are very
>> appreciated!
>>
>> cpp                 =  /lib/cpp
>> define              =  -DFLEXIBLE
>> constraints         =  none
>> integrator          =  l-bfgs
>> nsteps              = 50000000
>> ;
>> ;	Energy minimizing stuff
>> ;
>> emtol               =  0.000000001
>> emstep              =  0.000000001
>
>Your step size is too small
>
>standard are here (see handbook chapter 7.3):
>
>emtol = 100.0 [KJ/(mol nm)]
>emstep = 0.01 [nm]
>
>so try this and if it doesn`t work, change the standard parameters with factor 
>10 or 100.
>

>
>Greetings,
>
>Florian
>
>-- 
>-------------------------------------------------------------------------------
> Florian Haberl                        
> Computer-Chemie-Centrum   
> Universitaet Erlangen/ Nuernberg
> Naegelsbachstr 25
> D-91052 Erlangen
> Mailto: florian.haberl AT chemie.uni-erlangen.de
>-------------------------------------------------------------------------------
>
Thanks, Florian! But the optimization is not for MD but for NMA. So the emtol have to be 10-6 at least.

Best regards
Yechun