[gmx-users] CG energy minimization

[Xavier Periole]

On Mon, 14 Jan 2008 17:41:13 -0500
  "Myunggi Yi" <myunggi at gmail.com> wrote:
> Yes, I did (constraints=none).
> 
> These are my conclusions.
> 
> Since I could do CG without my position restraint,

Are you sure you do CG simulations? your includes indicates you don't!

> My .top doesn't include any constraint. (if my posre.itp is not constraint).
> The manual says "SD is enough for general purpose".
> If one wants to do energy minimization with position restraint, then do SD
> only.

You want to do stochastic dynamics (SD) or energy minimization (steep)?

Your message is confusing ...

XAvier
  
> 
> Thank you anyway.
> 
> 
> On Jan 14, 2008 5:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
>>
>> Perhaps this is too obvious to be the solution, but have you considered
>> setting
>> 'constraints = none' in your em.mdp file?  After all, as Mark originally
>> pointed out, the documentation will tell you that constraints and CG don't
>> mix.
>>
>> -Justin
>>
>> Quoting Myunggi Yi <myunggi at gmail.com>:
>>
>> > Sorry this is my top file.
>> >
>> > #include "ffgmx.itp"
>> > #include "../lipid.popc.itp"
>> > #include "popc.itp"
>> > #include "pro.itp"
>> > #include "ions.itp"
>> > #include "spc.itp"
>> >
>> > Which one defines constraints?
>> >
>> >
>> > On Jan 14, 2008 4:35 PM, Myunggi Yi <myunggi at gmail.com> wrote:
>> >
>> > > Thnak you.
>> > >
>> > > I don't use any constrant like lincs or shake.
>> > > Why do I get the error message.
>> > >
>> > >
>> > >
>> > > On Jan 14, 2008 4:11 PM, Mark Abraham < Mark.Abraham at anu.edu.au>
>> wrote:
>> > >
>> > > > Myunggi Yi wrote:
>> > > > > Dear users,
>> > > > >
>> > > > > I'd like to restraint the protein during the minimization.
>> > > > > I've got the following message.
>> > > >
>> > > > In GROMACS, restraints are different from constraints. Check out the
>> > > > manual for details.
>> > > >
>> > > > > ERROR: can not do Conjugate Gradients with constraints
>> > > >
>> > > > Your .top is defining some constraints, and if you'd checked out the
>> > > > manual, you'd have confirmed that GROMACS can't handle constraints
>> with
>> > > > the CG algorithm.
>> > > >
>> > > > > em.mdp file
>> > > > > +++++++++++++++++++++
>> > > > > cpp                      = cpp
>> > > > > include                  =
>> > > > > define                   = -DPOSRES
>> > > > > define                   = -DFLEXIBLE
>> > > > >
>> > > > > ; RUN CONTROL PARAMETERS
>> > > > > integrator               = cg
>> > > > > ; Start time and timestep in ps
>> > > > > tinit                    = 0
>> > > > > dt                       = 0.001
>> > > > > nsteps                   = 250
>> > > > > +++++++++++++++++++++
>> > > > >
>> > > > > How can I do this?
>> > > >
>> > > > Either don't use constraints or don't use CG.
>> > > >
>> > > > Mark
>> > > > _______________________________________________
>> > > > gmx-users mailing list     gmx-users at gromacs.org
>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > > > Please search the archive at http://www.gromacs.org/search before
>> > > > posting!
>> > > > Please don't post (un)subscribe requests to the list. Use the
>> > > > www interface or send it to gmx-users-request at gromacs.org.
>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Best wishes,
>> > >
>> > > MYUNGGI YI
>> > > ==================================
>> > > KLB 419
>> > > Institute of Molecular Biophysics
>> > > Florida State University
>> > > Tallahassee, FL 32306
>> > >
>> > > Office: (850) 645-1334
>> > > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> <
>> http://www.scs.fsu.edu/%7Emyunggi>
>> > >
>> >
>> >
>> >
>> > --
>> > Best wishes,
>> >
>> > MYUNGGI YI
>> > ==================================
>> > KLB 419
>> > Institute of Molecular Biophysics
>> > Florida State University
>> > Tallahassee, FL 32306
>> >
>> > Office: (850) 645-1334
>> > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
>> >
>>
>>
>>
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> ========================================
>> _______________________________________________
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>>
> 
> 
> 
> -- 
> Best wishes,
> 
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
>Florida State University
> Tallahassee, FL 32306
> 
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------