[gmx-users] strange but true : How to explain and avoid?

[Tsjerk Wassenaar]

Or:

sed -i '/gcq/d;/Thanx/d;' dump.out

on Mac:

sed -i.bck '/gcq/d;/Thanx/d;' dump.out

Cheers,

Tsjerk


On Tue, Jul 8, 2014 at 10:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/8/14, 4:02 PM, Chetan Mahajan wrote:
>
>> Hi Justin,
>>
>> If it's just gcq, then there is no problem to locate and remove. But as I
>> mentioned in one of the emails, there could be any other messages like
>> "Thanx
>> for Using GROMACS - Have a Nice Day". So detecting them and manually
>> removing them does not seem smooth. I think 2 > stderr.log seems the best
>> option.
>>
>>
> The "Thanx" message only shows up if you've disabled cool quotes, but
> regardless this is another simple grep -v statement.
>
> grep -v "gcq" dump.out | grep -v "Thanx" > dump_clean.out
>
> would take care of both, regardless of cool quotes settings.
>
> -Justin
>
>
>  Thanks
>> Chetan
>>
>>
>> On Tue, Jul 8, 2014 at 11:47 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/8/14, 12:44 PM, Chetan Mahajan wrote:
>>>
>>>  Hi Tsjerk,
>>>>
>>>> Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end of
>>>> the command seems the only way out, since, as I said, I am also getting
>>>> greeting messages in addition to gcq quotes. However, adding
>>>>  2>/dev/null
>>>>   will
>>>> also suppress unusual errors, if any at all. There does not seem a way
>>>> out
>>>> of this.
>>>>
>>>>
>>>>  Is there a reason these quotes or messages are causing a problem?  If
>>> you're simply dumping to a text file, a simple grep -v "gcq" will get rid
>>> of the quotes lines and you can continue doing whatever you were doing
>>> before.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.