[gmx-users] Disk Space

[teklebrh at ualberta.ca]

Dear Chris and Justin,

I just read the manual and it stated that I need a .trr file if I want  
to extend the simulation ( from 5ns -20ns).

My question is:

For the first 5ns I want to use berendsen thermostat and barostat so  
that my system will relax faster compared to N-H and P-R. Then I will  
switch on to the Nose-Hover and Parrinello-Rahman ( this will give me  
a correct description for the kinetic energy information.

Therefore, I need both coordinate and velocity files then ( Gromacs 3.3.3).

>>> nstxout                  = 50000
>>> nstvout                  = 50000
>>> nstfout                  = 0

>>> ; Output frequency for energies to log file and energy file
>>> nstlog                   = 2000
>>> nstenergy                = 1000
>>> ; Output frequency and precision for xtc file
>>> nstxtcout                = 2000
>>> xtc-precision            = 1000

rather than set the values of nstxout and  nstvout , if I set them to  
50000, I could get the .trr file. But for my entire analysis I will  
depend on the .xtc file.

step 1

after 5ns of my simulation( Both berendsen thermostat and barostat. I  
have to use still grompp to generate a new .tpr file by modifying the  
.mdp file ( t_ coupling,p_couple and the tinit). Once done this I run  
mdrun.

step 2

use the following procedure then after

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr  
-extend timetoextend

Am I correct? and also is the output file seems reasonable.

I am trying to balance both the disk space issue and what output I  
need to continue further.

Thank you chris and justine.

Rob




Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> teklebrh at ualberta.ca wrote:
>> Dear Chris,
>>
>> Thank you very much!
>>
>> I am planning to set the output control option like this!
>>
>> tinit               =  0
>> nstxout             =  2000
>> nstvout             =  0
>> nstfout             =  0
>> nstlog              =  2000
>> nstenergy           =  1000
>>
>> I want to set the velocity and force option to zero and save the  
>> coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By  
>> doing this am I missing anything.
>>
>
> Unless you need full-precision coordinates every few ps, you can use  
> nstxtcout = 2000 and set nstxout = 0.  A .xtc file is substantially  
> smaller than a .trr file.
>
> -Justin
>
>> regards,
>>
>> Rob
>>
>>
>>
>> Quoting chris.neale at utoronto.ca:
>>
>>> Dear Rob:
>>>
>>> To answer your question: just set up your run with nsteps for 5  
>>> ns, run mdrun, and then use tpbconv -until. A simpler option is to  
>>> set it up to run 20 ns, but use -maxh to limit it to an amount of  
>>> runtime that you pre-calculate to be similar to 5 ns of simulation.
>>>
>>> HOWEVER:
>>>
>>> You almost surely don't need to save this so often: nstxout = 100  
>>> (also nstvout, nstfout).
>>>
>>> And you may not even need to save this so often: nstxtcout = 100  
>>> (also nstenergy).
>>>
>>> I had no idea that there was an option nstcheckpoint = 100 as I  
>>> use mdrun -cpt 6 to specify a .cpt file every 6 hours, but there  
>>> is no need to write a .cpt every 100 steps.
>>>
>>>
>>>
>>> Dear Gromacs users,
>>>
>>> I am running an MD simulation but it looks to me that I am running out
>>> of disk space.
>>>
>>> This is my .mdp file
>>>
>>> ; OUTPUT CONTROL OPTIONS
>>>
>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>> nstxout                  = 100
>>> nstvout                  = 100
>>> nstfout                  = 100
>>> ; Output frequency for energies to log file and energy file
>>> nstlog                   = 100
>>> nstenergy                = 100
>>> ; Output frequency and precision for xtc file
>>> nstxtcout                = 100
>>> xtc-precision            = 100
>>> nstcheckpoint            = 100 ; checkpointing helps you continue
>>> after crashe. This checkpint file is saved every 1ns
>>>
>>>
>>> Please tell me which files i need to set zero.
>>>
>>> I am planning to run my simulation for 20ns but I want it to run every
>>> five nanoseconds until i see an aggregations in my system. So how can
>>> I re-start my simulation every 5ns.
>>>
>>>
>>> Thank you for your help
>>>
>>> rob
>>>
>>>
>>>
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>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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