[gmx-users] turn off pdb output

[Erik Lindahl]

Hi,

Ah, then it's probably because of the rerun. I bet we're never making  
a call to low_constrain with bInit set, which means the variable  
isn't set.

Try this:

  Edit low_constrain() in constr.c so to make bDumpOnError an integer  
instead of boolean, and initialize it to -1.

Then cell getenv() (which can be slow) outside the init part, but  
only if bDumpOnError==-1, and set it to 0 or 1. Finally edit the  
conditionals for bDumpOnError to check if it is 1 instead.

Cheers,

Erik



On Mar 22, 2007, at 5:30 PM, David Mobley wrote:

> Erik, Berk,
>
>> Hi David,
>>
>> It doesn't matter - we just check if it is set at all, i.e. whether
>> getenv("NO_SHAKE_ERROR") returns NULL or not.
>
> I still get PDB files written out due to shake errors using mdrun
> -rerun in 3.3 when running after doing "setenv NO_SHAKE_ERROR".
>
> David
>
>>
>> Cheers,
>>
>> Erik
>>
>>
>> On Mar 22, 2007, at 12:59 AM, David Mobley wrote:
>>
>> > Berk,
>> >
>> > What value does this need to be set to for it to work?
>> >
>> > Thanks,
>> > David
>> >
>> >
>> > On 3/20/07, Berk Hess <gmx3 at hotmail.com> wrote:
>> >>
>> >> There seems to be an environment variable NO_SHAKE_ERROR
>> >>
>> >> Berk.
>> >>
>> >>
>> >> >From: "David Mobley" <dmobley at gmail.com>
>> >> >Reply-To: Discussion list for GROMACS users <gmx- 
>> users at gromacs.org>
>> >> >To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> >> >Subject: [gmx-users] turn off pdb output
>> >> >Date: Mon, 19 Mar 2007 10:28:42 -0700
>> >> >
>> >> >All,
>> >> >
>> >> >Under some circumstances, mdrun writes out pdb files with
>> >> previous and
>> >> >current coordinates. Is there some way I can turn this off?
>> >> >
>> >> >For reasons I'd rather not explain, I'm reprocessing a single
>> >> >precision trajectory using the double precision version of mdrun,
>> >> and
>> >> >this results in pdb files being written every step. For obvious
>> >> >reasons, I would like to avoid this.
>> >> >
>> >> >Thanks,
>> >> >David
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