[gmx-users] Question: KALP-15 in DPPC tutorial

[Justin Lemkul]

The output frequency is far too large for normal usage.  Reduce the output 
frequency by increasing the values of nstxout and nstvout, or simply set them to 
zero to suppress .trr writing (it's not useful for most normal quantities).

-Justin

On 7/12/16 12:38 PM, Tapash, Arifuzzaman wrote:
> Hi all,
>
> I'm very new in Gromacs. I have completed the Lysozyme in water tutorial (by Justin A. Lemkul) successfully. Now I'm doing the KALP-15 in DPPC.
>
> I have successfully done the equilibration stage (both temperature and pressure). I have a question about the npt.trr file.
>
> After completing the pressure equilibration, the npt.trr file was generated which is about 17 GB size, provided the equilibration was done for 1 ns (I used all the *.mdp file provided there, didn't do any change) and I followed all the procedure mentioned in the tutotial. During the solvation process I used 1.0 nm distance of box side (gmx editconf -f *.gro -o *.gro -c -d 1.0 -bt cubic).
>
> 1) My question is, is the file size (17 GB - npt.trr) normal? Or I did any mistake during previous steps?
>
> I am concerned because, the cluster I'm using, they provide only 25 GB space. So, if for some reason, I have to do the equilibration for longer time, it will produce a bigger file.
>
>
> 2) My another concern is, will the 'Production MD' step will produce a very large file (larger than 25 GB)?
>
> I'm sorry, these might be very silly question, and I know all of you are very busy with your work.
>
> Thanks for taking time to help me.
>
> Arifuzzaman Tapash
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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