[gmx-users] groups to write to trr

[Vitaly Chaban]

Shay,

Thanks. trjconv is good but we need to reduce the volume of TRR in such a way.

When you calculate VACFs (velocities are written every 5 or 10 fs and
the system size is 10 000 particles or more), the trr files with all
atoms in the system could be more than 10 Gb. And if one runs a series
of such tasks it's very tricky to find so much free space on the
cluster.
We are simply out of place. :(

Dear Developers,
Please make a key to control TRR output in the next release.

Thank you very much.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban


2008/8/23 Shay Amram <shayamra at post.tau.ac.il>:
> I think you should try using:
>
> trjconv –f file.trr –o file_with_groups_of_interest.trr –n index.ndx
>
>
>
> You should create the relevant index group (that includes all atoms of
> interest)  before invoking the above command. You'll be prompted to choose a
> group so choose the group you created and trjconv will write an output trr
> that includes the group you picked alone.
>
>
>
> Hope that helps.
>
> -Shay
>
>
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Vitaly Chaban
> Sent: Friday, August 22, 2008 14:05 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] groups to write to trr
>
>
>
> Hi,
>
>
>
> Is it possible to write only the specified groups to the TRR
>
> trajectory like using xtc-grps key for XTC?
>
>
>
> We calculate VACFs and so need velocities to be written but only the
>
> velocity of some groups are of interest, not of all the particles. The
>
> "full" TRRs take extremely huge space...
>
>