[gmx-users] Disk Space

[Justin A. Lemkul]

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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