[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Anurag Dobhal]

Dear justin

Thank you for your rely and precious time.

I am aware that .gro file is to be visualized in VMD and its content can be
checked in text editor.
all the previous .gro file are visualized and checked in VMD.

I have obetained that ( confout.gro )file by running the command of energy
minimization i.e.

"mdrun -v -deffnm em"

and before this command I ran the command

"perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"


after running the energy minimization the confout.gro is actually obetained as

confout.gro.trr. so I am renaming it as confout.gro. so it is actually
.trr format, which can not be visualised in VMD or checked in text
editor.

Please help.


On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/30/14 7:06 AM, Anurag Dobhal wrote:
>
>> Thank you Justin for your reply
>>
>> as per your suggestion i verified the contents in confout.gro but i was
>> unable to check file as when i am clicking on it to open it I am getting
>> an
>> message that file is of unknown type.
>>
>>
> A .gro file is not simply something that you click on to magically open.
> It's just a listing of coordinates.  Visualize it in VMD.  Inspect its
> contents with a text editor.
>
> -Justin
>
>
>  I again repeated the tutorial and I am getting the same things.
>>
>> Thank you again for your time.
>>
>> On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/30/14 5:51 AM, Anurag Dobhal wrote:
>>>
>>>  Hello gromacs users.
>>>>
>>>>
>>>> I am running GROMACS Tutorial of  KALP15 in DPPC.
>>>>
>>>> I am in the step define box and solvate.
>>>>
>>>> after the command
>>>>
>>>> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
>>>> area_shrink1.dat
>>>>
>>>>
>>>> i am getting an error as
>>>>
>>>> Use of uninitialized value $box_x in multiplication (*) at
>>>> inflategro.pl line 339.
>>>> Use of uninitialized value $box_y in multiplication (*) at
>>>> inflategro.pl line 340.
>>>> Scaling lipids....
>>>> There are 0 lipids...
>>>> Illegal division by zero at inflategro.pl line 380.
>>>>
>>>> I am repeating the step third time and I am getting the same error.
>>>>
>>>> please help me how to skip this error.
>>>>
>>>>
>>>>  I suggested you verify the contents of confout.gro are sensible.  What
>>> did
>>> you learn?
>>>
>>> -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
>>>
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>>
> --
> ==================================================
>
> 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
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