[gmx-users] Few general questions.

[David]

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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