[gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

[Anurag Dobhal]

Hey gromacs users

I got the confout.gro file by running the command

mdrun -v -deffnm em -o confout.gro

and then i ran the command " perl inflategro.pl confout.gro 0.95 DPPC
0 system_shrink1.gro 5 area_shrink1.dat "

but now the teminal says that

Reading.....
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


is this output is expected ???


please guide me.


Thank you




On Sun, Sep 28, 2014 at 6:33 PM, Anurag Dobhal <
anurag.dobhal at nano-medicine.co.in> wrote:

> Dear users.
>
>
> I am doing the tutorial "KALP15 in DPPC".
>
> I heve done till the command
>
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
> and then i minimised the the system by running the command
>
> mdrun -v -deffnm em
>
> now i am unable to understand how to produce "confout.gro"
>
>
> please help how to proceed and where I am wrong.
>
>
> Thank you
>
>
> Anurag Dobhal
>
>
> On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal <
> anurag.dobhal at nano-medicine.co.in> wrote:
>
>> Dear users.
>>
>>
>> I am doing the tutorial "KALP15 in DPPC".
>>
>> I heve done till the command
>>
>> "genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000
>> 100000"
>>
>> after that I am not able to understand wat to do and how to solvate the
>> system.
>>
>> please can anyone expalin me in easy words how to proceed.
>>
>> Please help
>>
>>
>> Anurag Dobhal
>>
>>
>>
>>
>>
>>
>

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