[gmx-users] Few general questions.

[Itamar Kass]

      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

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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> -- 
> 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
============================================

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