[gmx-users] Reducing trr storage volume

Mark Abraham mark.j.abraham at gmail.com
Sun Jan 6 22:23:13 CET 2013

You can construct such a subset after the fact by using trjconv with (say)
an index group created with g_select, but you will have to script that
process frame by frame yourself.


On Fri, Jan 4, 2013 at 9:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 1/4/13 11:09 AM, Shima Arasteh wrote:
>> Dear users,
>> I'm simulating a system of protein/water/popc/ions. The peptide is
>> inserted through the transmembrane, and the peptide acts as a channel.
>> In order to reduce the trajectory storage volume, I need to use xtc-grps
>> in .mdp file. In my system, I'd rather to store the positions of
>> peptide,ions and waters "near" the peptide (I mean a specific region near
>> the peptide: entrances of peptide + through the peptide).The large amount
>> of water molecules positions exist up and down the bilayer, are not
>> expected to be saved.
>> I'm wondering if it is possible to chose a specific region in xtc-groups?
>> Or any other solution to reduce the storage volume of trr file?
> I doubt you can achieve such a group consistently.  Water molecules will
> diffuse over time.  Index groups provided to grompp can only be specified
> to be a fixed size and cannot be dynamically created to satisfy any
> geometric criterion during mdrun.  Thus, your initial group may indeed
> represent the desired molecules, but over time, the waters within the group
> will (likely) drift away and may not be anywhere near the original position.
> If your system contains a lot of water that you deem unnecessary, perhaps
> you should consider the manner in which the system was constructed...
> The only way to decrease the size of a .trr file is to decrease nstxout,
> nstvout, and/or nstfout.  For various technical reasons, there is no way to
> save only a subset of atoms in .trr format.  Refer to previous discussions
> on this topic.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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