[gmx-users] re: Unreadable trajectory [solved]

[Jernej Zidar]

>
> Writing 100,000 or 100.000 for 100000 is prone to misinterpretation. Get
> out of the habit of using a thousands separator in scientific contexts :-)

Thanks for the advice.

>
>>
>> 2. Remove contraints and repeat steps a-h.
>>
>>    The problem I'm having is that I cannot visualize the trajectories
>> from step 2.e) onwards with VMD simply segfaulting. While it may well
>> be a VMD issue but I can't visualize the trajectory using ngmx (blank
>> screen) either, so it's an issue either with my inputs or Gromacs.
>
> Your .mdp file is not writing any trajectory frames.

Thanks for pointing that out! It was writing only information on velocities.

 I'm still getting used to the GROMACS way of doing things. One input
(i.e. MDP file) for each run and all that.

>
> Mark
>
>>
>>    I tried to use trjconv tool to adjust the centering or remove the
>> PBC or save just the polymer residues but the utility always fails
>> with: WARNING no output, last frame read at t=200.
>>    Checking the run log file did not reveal any errors. Checking the
>> EDR file revealed no jumps in any of the enery terms.
>>
>>    What's most surprising, is that I can visualize the GRO file that is
>> generated at the end of the simulation.
>>
>>    The relevant files are on the following links:
>> - MDP: http://dl.dropbox.com/u/5761806/md-nvt-2-nofix.mdp
>> - LOG: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.log
>> - TPR: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.tpr
>>
>>     I use GROMACS 4.5.5, the system is electrically neutral. To prepare
>> a new TPR file a use the GRO file from the previous run.
>
> Don't, you're losing precision and introducing perturbations. grompp -t
> old.cpt is your friend.
>
> Mark

Using that. Many many thanks!

Thanks for the help,
Jernej Zidar