[gmx-users] glibc detected *** g_sas_d

[Justin Lemkul]

On 7/18/13 8:04 AM, Rasoul Nasiri wrote:
> Justin,
>
> I just ran this calculations on "VERSION 4.6-GPU-dev-20120501-ec56c" and I
> will let you know about the outcomes.
>

The outcome of 4.6.3 would be more interesting than an outdated development version.

-Justin

> Rasoul
>
>
> On Thu, Jul 18, 2013 at 1:09 PM, Rasoul Nasiri <nasiri1355 at gmail.com> wrote:
>
>> Bellow are commands and error message:
>>
>> 1-   trjconv_d -f traj.xtc -n maxclust.ndx -o traj_out.xtc
>>
>> 2-    g_sas_d  -f  traj_out.xtc  -n maxclust.ndx  -o surface.xvg  -nopbc
>>
>>
>> glibc detected *** g_sas_d: malloc(): memory corruption:
>> 0x00000000016dfcd0
>>
>>
>> Rasoul
>>
>>
>> On Thu, Jul 18, 2013 at 1:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 7/18/13 6:52 AM, Rasoul Nasiri wrote:
>>>
>>>> Hello all,
>>>>
>>>> I'm trying to know how the surface area of a nano-drop changes during the
>>>> evaporation in the vacuum.
>>>>
>>>> When I filter the trajectory of non-evaporated molecules by trjconv and
>>>> use
>>>> g_sas for calculation of their surface, it usually crash (I'm using
>>>> version
>>>> of 4.5.5).
>>>>
>>>>
>>> What's the error message?  What's your command?
>>>
>>>
>>>   Is there still this issue in the 4.6.*? How it can be resolved?
>>>>
>>>>
>>> Have you tried version 4.6?  That's the quickest way to know.  If there
>>> are still problems, you'll need to provide more information.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================**====================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> 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 <jalemkul at outerbanks.umaryland.edu>| (410) 706-7441
>>>
>>> ==============================**====================
>>> --
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>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
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

==================================================