[gmx-users] Running iteration for lipid shrinking using InflateGRO methodology

[Justin Lemkul]

On 9/27/19 12:53 PM, Yogesh Sharma wrote:
> hello users,
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> I am using inflategro methodology  to pack lipids around membrane protein.
> I used bash script for iteration cycle provided by Justin Lemkul
> *. *
> But unexpectedly, cycle is dying here
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> *gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro
> -pbc molWill write gro: Coordinate file in Gromos-87 formatReading file
> system_inflated_em.tpr, VERSION 5.1.2 (single precision)Reading file
> system_inflated_em.tpr, VERSION 5.1.2 (single precision)Select group for
> outputGroup     0 (         System) has  9330 elementsGroup     1 (
>   Protein) has  2882 elements.....................Group    12 (
>   Other) has  6448 elementsGroup    13 (           POPC) has  6448
> elementsSelect a group: Selected 0: 'System'Reading frames from gro file
> 'POPC', 9330 atoms.Reading frame       0 time    0.000   Precision of
> system_inflated_em.gro is 0.001 (nm)Using output precision of 0.001
> (nm)Last frame          0 time    0.000
> ########################################## RUNNING SHRINKING ITERATION
> {1..26}...#########################################run_inflategro.sh: 32:
> run_inflategro.sh: Illegal number: {1..26}*

Perhaps your version of Bash doesn't like the way I've done the 
iterating. You can use a seq command instead.

-Justin

> I used given ( justin lemkul
>
> minim_inflategro.mdp)
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> with nstlist modified to 10.
>   where is it going wrong.
> Previous commands:
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> gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top
> -r system_inflated.gro -o system_inflated_em.tpr
>
> gmx mdrun -deffnm system_inflated_em
>
> gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o
> tmp.gro -pbc mol
> mv tmp.gro system_inflated_em.gro
>
> perl inflategro.pl system_inflated_em.gro 0.95 DPPC 0
> system_shrink1.gro 5 area_shrink1.dat
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> sh run_inflategro.sh

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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