[gmx-users] Few general questions.

Itamar Kass ikass at cc.huji.ac.il
Sat Sep 13 11:12:01 CEST 2003

   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).

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?

3.Connected to the previous question, how do I know if the SHAKE/LINCS
algorithms work?  How can I activate/deactivate them if I want to (using the mdp
option or mdrun flag)?

                   Thanks all, Itamar.

Computers are like airconditioners... They don't work well with Windows

| 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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