[gmx-users] Few general questions.

[David]

On Sat, 2003-09-13 at 12:36, Itamar Kass wrote:
>       Hi David, I thank for the tip regarding the end time of the run, but I
> didn't understand what you meant regarding my third question.  As much as I
> understand the manual, the LINCS algorithm is automatic activate in any run for
> the hydrogen which are present (like in the HIS residues or in the water) 
>                    Kass

there is an option
constraints = none / h-bonds / all-bonds / h-angles / all-angles



> 
> Quoting David <spoel at xray.bmc.uu.se>:
> 
> > On Sat, 2003-09-13 at 11:10, Itamar Kass wrote:
> > >    Dear all, I am working with GROMACS for some time, and I have gather
> > some
> > > questions. I will appreciate if someone will have the time to answer my
> > questions.
> > > 
> > > 1.When I run mdrun I use the flag -v to see the time left until the
> > simulation
> > > end.  But when I do long simulations, I close the terminal from which I run
> > the
> > > program. Hence I do not know when the simulation will end (I know I can do
> > rough
> > > calculation using the md.log).  I wanted to know if there is a command
> > which
> > > tells the program to write into a file this data (I tried mdrun -v .. >
> > time.log).
> > > 
> > use mdrun >& logfile
> > 
> > > 2.I work upon a system of a peptide embedded in a membrane, what is the
> > largest
> > > time step I can use?  For now I use time step of 2fs, although I saw other
> > use
> > > time step of 5fs (for membrane), is it O.K. To use such large time step?
> > > 
> > You will have to use dummies for your protein (check papers by Feenstra
> > et al.) pdb2gmx -dummy hydrogen. Erik L and me have a paper coming up in
> > JPC B where we compare long simulations of a protein in water with and
> > without dummies, and there is basically no difference.
> > 
> > 
> > > 3.Connected to the previous question, how do I know if the SHAKE/LINCS
> > > algorithms work?  How can I activate/deacti
> > > vate them if I want to (using the mdp
> > > option or mdrun flag)?
> > > 
> > constraint algorithm  = shake or lincs
> > 
> > 
> > >                    Thanks all, Itamar.
> > > 
> > > 
> > > ********************************************
> > > Computers are like airconditioners... They don't work well with Windows
> > > open.
> > > ********************************************
> > > 
> > > ===========================================
> > > | Itamar Kass
> > > | The Alexander Silberman
> > > | Institute of Life Sciences
> > > | Department of Biological Chemistry
> > > | The Hebrew University, Givat-Ram
> > > | Jerusalem, 91904, Israel
> > > | Tel: +972-(0)2-6585146
> > > | Fax: +972-(0)2-6584329
> > > | Email: ikass at cc.huji.ac.il
> > > | Homepage:
> > http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> > > ============================================
> > > 
> > > -------------------------------------------------
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> > > _______________________________________________
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> > -- 
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> > 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
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> > 
> 
> 
> 
> 
> ********************************************
> Computers are like airconditioners... They don't work well with Windows
> open.
> ********************************************
> 
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585146
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> ============================================
> 
> -------------------------------------------------
> This mail sent through IMP: http://horde.org/imp/
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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