[gmx-users] groups to write to trr

[Justin A. Lemkul]

Shay Amram wrote:
> 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.
> 
>  

Is this the problem, or is the problem that your disk is getting dangerously 
full during the simulation?

The risk you take with specifying trr-grps in an .mdp file is if your simulation 
goes down (i.e., hardware failure, power outage).  If you haven't written the 
whole system to the .trr file, you risk losing (potentially) a lot of computing 
time.

-Justin

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

Justin A. Lemkul
Graduate Research Assistant
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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