[gmx-users] Few general questions.

David spoel at xray.bmc.uu.se
Sat Sep 13 12:06:01 CEST 2003

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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