[gmx-users] Timestep

[Xavier Periole]

It is not possible to answer your question from the information you give.
A lot of things can cause a segmentation fault. From compilation to
your particular system. Put a search on the user-list, you'll get an idea
of possible problems.

It depends what you will be looking at but I would suggest to stick
to a 2 fs time step.

XAvier

>  Thanks to Xavier for his prompt reply..
> 
>  Actually my objective is a bit longer[50-60ns] but the problem is that
> even if i cant change the time-step to 0.003 it is exiting saying
> segmentation fault then how is it possible with 1fs [or 4 fs as
> suggested] which i want to do to reduce time.
>  I wanted to know where the problem is... why cant i increase the time
> step and the only error shown is 'segmentation fault'..so is the reason
> in compilation or coding or machine precision or is it with molecular
> system wise thats what i was trying to understand..
> 
> Thanks again..
> Ramya.
> 
>>
>> 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
>>>
>>>
>>>
>>> *********$$$*********
>>>
>>> Ramya Cherukupalli,
>>>Final year,
>>> M.S Bioinformatics,
>>> IIIT - H.
>>>
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> -----------------------------------------------------
>> XAvier Periole - PhD
>>
>> 1- Institute of Molecular Assemblies
>>       City University of New York - USA
>> 2- Molecular Dynamics-Group
>>       University of Groningen - The Netherlands
>> http://md.chem.rug.nl/~periole
>> -----------------------------------------------------
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
> 
> 
> *********$$$*********
> 
> 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
-----------------------------------------------------