ngs and not the symptoms
is wise.
Mark
Date: Mon, 30 Jan 2012 22:25:48 +1100
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] simulation killed
On 30/01/2012 9:56 PM, mura
oceed with a script that you can now have confidence in.
-Justin
> Date: Mon, 30 Jan 2012 21:26:20 +0800
> Subject: Re: [gmx-users] simulation killed
> From: lina.lastn...@gmail.com
> To: gmx-users@gromacs.org
>
> On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul
wrote
lina ı didn't write this script.. script is on free energy tutorial 6 by
justin a. lemkul
ı changed to my own business.. would like to calculate deltaGbinding for
protein ligand complexes
> Date: Mon, 30 Jan 2012 21:26:20 +0800
> Subject: Re: [gmx-users] simulation killed
> Fr
;> # NPT EQUILIBRATION #
>>> #
>>> echo "Starting constant pressure equilibration..."
>>>
>>> cd ../
>>> mkdir NPT
>>> cd NPT
>>>
>>> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA
GY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
-maxwarn 3
mdrun -nt 8 -deffnm md$LAMBDA
echo "Production MD complete."
# End
echo "Ending. Job completed for lambda = $LAMBDA"
Date: Mon, 30 Jan 2012 13:54:18 +0800
Subject: Re: [gmx-users] simulation killed
From: lina.l
>
> mdrun -nt 8 -deffnm npt$LAMBDA
>
> echo "Constant pressure equilibration complete."
>
>
> #
> # PRODUCTION MD #
> #
> echo "Starting production MD simulation..."
>
> cd ../
> mkdir Production_MD
> c
.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] simulation killed
On 30/01/2012 9:56 PM, murat özçelik wrote:
hi! lina my script this please tell me where is
wrong...thanks
Probably your u
.gro
-p $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o
md$LAMBDA.tpr -maxwarn 3
mdrun -nt 8 -deffnm md$LAMBDA
echo "Production MD complete."
# End
echo "Ending. Job completed for lambda = $LAMBDA"
> Date: Mon, 30 Jan 2012 13:54:18 +0800
> Subject: Re: [gmx-user
lete."
# End
echo "Ending. Job completed for lambda = $LAMBDA"
> Date: Mon, 30 Jan 2012 13:54:18 +0800
> Subject: Re: [gmx-users] simulation killed
> From: lina.lastn...@gmail.com
> To: gmx-users@gromacs.org
>
> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik
>
mpleted for lambda = 0
> mkiytak@babil:~/JOB1$
>
>
> How can I solve this problemthanks for your help.
>
>
>
>
>
>
>
>> Date: Sun, 29 Jan 2012 10:43:53 -0600
>> From: p...@uab.edu
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-user
777 Killed mdrun -nt 8 -deffnm md$LAMBDA
Production MD complete.
Ending. Job completed for lambda = 0
mkiytak@babil:~/JOB1$
How can I solve this problemthanks for your help.
> Date: Sun, 29 Jan 2012 10:43:53 -0600
> From: p...@uab.edu
> To: gmx-users@gromacs.org
> S
something killed your job but it wasn't gromacs.
Your system has run time or memory requirements that your job exceeded.
On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote:
> hi! all
>
> ı have to a big problem..ı am doing free energy calculation for a ligand (L
> histidine ) when ı perform mdru
hi! all
ı have to a big problem..ı am doing free energy calculation for a ligand (L
histidine ) when ı perform mdrun .. my simulation stop ... the program gave
me this message..
Reading file md0.tpr, VERSION 4.5.4 (single precision)
Starting 8 threads
Making 1D domain decomposition 8 x 1 x 1
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