[gmx-users] Obtaining energies from trr files

Chng Choon Peng cpchng at bii.a-star.edu.sg
Tue Mar 30 10:10:02 CEST 2004

Dear David,

   Thanks for the reply.

I heard about -rerun option in mdrun but never used it.
Tried it just now and run into errors:

% mdrun -s md.tpr -rerun md_WAT_7.xtc

Reading file md.tpr, VERSION 3.1.5_pre1 (single precision)
starting md rerun 'Protein in water', reading coordinates from input
trajectory 'md_WAT_7.xtc'

Reading frame       0 time    0.000
WARNING: Some frames do not contain velocities.
         Ekin, temperature and pressure are incorrect,
         the virial will be incorrect when constraints are present.

Segmentation fault

I modified one of the energy 'tc_grps' and added a new one.
Repeated for 'energygrps' as well.

Yes, my trajectory files do not contain velocities nor forces:
nstxout             =  5000     ; collect data every 10 ps
nstvout             =  0
nstfout             =  0

But I should still be able to get vdW and coulomb which only depends on
separation, right?

Thanks again.


On 3/30/04 1:32 PM, "David" <spoel at xray.bmc.uu.se> wrote:

> On Tue, 2004-03-30 at 02:44, Chng Choon Peng wrote:
>> Dear all,
>>    Is it possible to recover vdW & Coulomb energies between a group of atoms
>> (not defined as an energy group for MD) and rest of protein from the
>> trajectory file of positions information?
>> It was an after-thought to want to compute the interaction energies.
>> Or there is no other way but to re-run the simulation?
> Hang on, you do know about the mdrun -rerun option, don't you?
>> Any help is greatly appreciated. :)
>> regards,
>> Choon-Peng
>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596,      75124 Uppsala, Sweden
>phone:    46 18 471 4205        fax: 46 18 511 755
>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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