[gmx-users] trjconv_d errors

[Mark Abraham]

On Mon, Apr 6, 2015 at 2:51 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

>
> Dear All,
>
> I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping
> there was adifference) as I am using terra grid with a 5.0.1 install.
>

We write release notes so that you can know what you're doing, rather than
hope...


> Now, I noticed 2 things, trjconv_d no matter what I do can not read or
> convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files.
>

You're doing something wrong, but without a detailed description of input
commands and output, nobody can help. "cannot read" and "cannot convert"
are two completely different things, and look different on your terminal.
Use gmx check on the trajectory files to be sure they contain what you
think they do.


>   I was simply interested mostly as my secound problem is, if I include
> anything other than the standard energy groups of protein non_protein (say
> x y z), the performance goes from 20 ns a day for my system, to 10 ns a
> day.  Thus I was going to rerun everything after the grid usage with -rerun
> and a changed energy group list just to make my life easier.
>

Wildly unlikely. You are surely varying something else as well. The general
policy of doing reruns afterwards is an efficient one, however.

I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f
> in.trr -o out.trr or out.xtc works fine.  It will even process a standard
> 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I
> get a version error.
>

*what* version error? from what command? there's no version number in a
.trr file, so you can't get "a version error" from doing a rerun on a .trr.

Is this a) a bug and b) a if so or not, does someone have a work around?
>

Can't tell, you haven't been precise enough, I'm afraid.

Mark


> I have also tried gmx_d trjconv, and I searched the mail archives, and the
> only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema,
> stating if the files were larger than a few gigs, there was a memory
> error.  I origionally thought this the error, however decided to run test
> first with small 100MB-2 G runs to test it, and this was not the problem.
>
> Sincerely,
>
> Stephan L. Watkins, PhD
>
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