[gmx-users] Timestep

[Xavier Periole]

10 ns of a solvated protein of regular size should not require much
computing time.

Increasing the time-step above 2 fs is a solution to increase the
speed of the run but then you face the problem of not integrating
the fast movement correctly and this can end up in large forces
and then you run crashes.
You could use dummy hydrogens (see manual) and heavy water and
use a 4 fs time step. This is ok for a simple protein in a box
of water.

But again 10ns of a protein solvated is not a long simulation.

XAvier
> 
>    I am trying to perform a simulation run of 10ns for my system
> [protein+waterbox].The system works fine if i use timestep[dt=0.002
> fs].   To balance the run time and time-consumption, when we try a
> .mdp file with slight increase of timestep i.e., to 0.003 fs; grompp
> works fine and generates input tpr, but when going further with mdrun,
> the program crashes, giving error:
>     "Segmentation Fault"
> 
> So i have to increase the number of steps[nsteps] to achieve required run
> time.But this'll be time consuming.I am unable to figure out any
> alternative.
> I am using Gromacs 3.3 on IBM Power5 machine with SLES9.
> Please suggest me the required to be done.Thanks in advance.
> 
> The .mdp file i've used:
> 
> integrator               = md
> ;Total simulation time: 5000 ps
> :time step in femtoseconds
> dt                       = 0.002
> ;number of steps
> nsteps                   = 2500000
> nstxout                  = 100
> nstvout                  = 100
> nstlog                   = 10
> nstenergy                = 10
> nstxtcout                = 10
> ;xtc_grps                = prot
> ;group(s) to write to energy file
> energygrps               = protein non-protein
>Frequency to update the neighbor list (and the long-range forces,
> ;when using twin-range cut-off's).
> nstlist                  = 10
> cut-off distance for the short-range neighbor list
> rlist                    = 0.8
> ;treatment of electrostatic interactions
> coulombtype              = PME
> rcoulomb                 = 0.9
> 
> 
> 
> *********$$$*********
> 
> Ramya Cherukupalli,
>Final year,
> M.S Bioinformatics,
> IIIT - H.
> 
> 
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-----------------------------------------------------
XAvier Periole - PhD

1- Institute of Molecular Assemblies
      City University of New York - USA
2- Molecular Dynamics-Group
      University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------