Re: [gmx-users] problem in running job.sh for free energy calculations.

[neelam wafa]

Thanks sir Mark and Justin.
I ll try to figure it out with the administer. But  in case the problem is
not resolved, is it okay if I run the commands directly through terminal?
Will it effect the results?
I know it ll be a tedious job.

Regards
Neelam Wafa

On Mon, 9 Apr 2018 10:03 pm Justin Lemkul,  wrote:

>
>
> On 4/9/18 12:56 PM, neelam wafa wrote:
> > Thanks Sir for your quick response.
> > These are the errors I am getting.
> > Error in user input:
> > Invalid command-line options
> >In command-line option -f
> >  File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not
> exist
> > or
> >  is not accessible.
> >In command-line option -c
> >  File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does
> not
> >  exist or is not accessible.
> >In command-line option -p
> >  File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist
> or
> > is
> >  not accessible.
> > job.sh: line 30: mdrun: command not found
> >
> >
> > Error in user input:
> > Invalid command-line options
> >In command-line option -f
> >  File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist
> or
> > is
> >  not accessible.
> >In command-line option -p
> >  File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist
> or
> > is
> >  not accessible.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > job.sh: line 65: mdrun: command not found
> >
> > similar errors I get for all the sets.
>
> It seems that the compute node has no idea where your files or
> executables are, which means however you've configured your job script
> is incorrect for your cluster. Consult your system administrator, as
> none of these problems are actually specific to GROMACS.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] problem in running job.sh for free energy calculations.

[Justin Lemkul]

On 4/9/18 12:56 PM, neelam wafa wrote:

Thanks Sir for your quick response.
These are the errors I am getting.
Error in user input:
Invalid command-line options
   In command-line option -f
 File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not exist
or
 is not accessible.
   In command-line option -c
 File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does not
 exist or is not accessible.
   In command-line option -p
 File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or
is
 not accessible.
job.sh: line 30: mdrun: command not found


Error in user input:
Invalid command-line options
   In command-line option -f
 File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist or
is
 not accessible.
   In command-line option -p
 File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or
is
 not accessible.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
job.sh: line 65: mdrun: command not found

similar errors I get for all the sets.


It seems that the compute node has no idea where your files or 
executables are, which means however you've configured your job script 
is incorrect for your cluster. Consult your system administrator, as 
none of these problems are actually specific to GROMACS.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] problem in running job.sh for free energy calculations.

[neelam wafa]

Hi

This is how I modified the job.sh script

#!/bin/bash

# Set some environment variables
FREE_ENERGY=/home/Downloads/Free_Energy
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP
echo ".mdp files are stored in $MDP"

LAMBDA=0

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

#
# ENERGY MINIMIZATION 1: STEEP  #
#
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM_1
cd EM_1

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o
min$LAMBDA.tpr

mdrun -nt 2 -deffnm min$LAMBDA

sleep 10

#
# ENERGY MINIMIZATION 2: L-BFGS #
#

cd ../
mkdir EM_2
cd EM_2

# We use -maxwarn 1 here because grompp incorrectly complains about use of
a plain cutoff; this is a minor issue
# that will be fixed in a future version of Gromacs
gmx grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p
$FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr -maxwarn 1

# Run L-BFGS in serial (cannot be run in parallel)

mdrun -nt 1 -deffnm min$LAMBDA

echo "Minimization complete."

sleep 10

#
# NVT EQUILIBRATION #
#
echo "Starting constant volume equilibration..."

cd ../
mkdir NVT
cd NVT

gmx grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p
$FREE_ENERGY/Methane/topol.top -o nvt$LAMBDA.tpr

mdrun -nt 2 -deffnm nvt$LAMBDA

echo "Constant volume equilibration complete."

sleep 10

#
# NPT EQUILIBRATION #
#
echo "Starting constant pressure equilibration..."

cd ../
mkdir NPT
cd NPT

gmx grompp -f $MDP/NPT/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p
$FREE_ENERGY/Methane/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr

mdrun -nt 2 -deffnm npt$LAMBDA

echo "Constant pressure equilibration complete."

sleep 10

#
# PRODUCTION MD #
#
echo "Starting production MD simulation..."

cd ../
mkdir Production_MD
cd Production_MD

gmx grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p
$FREE_ENERGY/Methane/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr

mdrun -nt 2 -deffnm md$LAMBDA

echo "Production MD complete."

# End
echo "Ending. Job completed for lambda = $LAMBDA"



On Mon, Apr 9, 2018 at 4:56 PM, neelam wafa  wrote:

> Thanks Sir for your quick response.
> These are the errors I am getting.
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not
> exist or
> is not accessible.
>   In command-line option -c
> File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does not
> exist or is not accessible.
>   In command-line option -p
> File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist
> or is
> not accessible.
> job.sh: line 30: mdrun: command not found
>
>
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist
> or is
> not accessible.
>   In command-line option -p
> File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist
> or is
> not accessible.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> job.sh: line 65: mdrun: command not found
>
> similar errors I get for all the sets.
>
> Regards
> Neelam Wafa
>
>
>
>
> On Mon, Apr 9, 2018 at 3:30 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 4/9/18 11:25 AM, neelam wafa wrote:
>>
>>> Dear sir Justin
>>>
>>> I am doing your tutorial of free energy calculations for methane in
>>> water.
>>> I have created the .mdp  and  .sh files using the perl script you
>>> provided.
>>> I have also made the FREE_ENERGY and MDP directories as in the job. sh
>>> script. gro file and topology files are also in the relevant folder but
>>> when I run job.sh script with command bash job.sh, it says the files the
>>> .mdp file, the methane_water.gro file and topol.top file either dont
>>> exist
>>> or not accessible. I have checked the files are in their proper places
>>> and
>>> are searched on terminal and opened though comand with vi editor. I have
>>> also given chmod 777 permission to these files. but no way out of the
>>> problem. please help me out. I have been searching the archive and google
>>> for the last three days but could not sort out. When i run the grompp and
>>> gmx md run commands directly through the terminal it works but not
>>> through
>>> the job.sh.
>>> Please suggest me a solution. Sorry for the 

Re: [gmx-users] problem in running job.sh for free energy calculations.

[neelam wafa]

Thanks Sir for your quick response.
These are the errors I am getting.
Error in user input:
Invalid command-line options
  In command-line option -f
File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not exist
or
is not accessible.
  In command-line option -c
File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does not
exist or is not accessible.
  In command-line option -p
File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or
is
not accessible.
job.sh: line 30: mdrun: command not found


Error in user input:
Invalid command-line options
  In command-line option -f
File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist or
is
not accessible.
  In command-line option -p
File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or
is
not accessible.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
job.sh: line 65: mdrun: command not found

similar errors I get for all the sets.

Regards
Neelam Wafa




On Mon, Apr 9, 2018 at 3:30 PM, Justin Lemkul  wrote:

>
>
> On 4/9/18 11:25 AM, neelam wafa wrote:
>
>> Dear sir Justin
>>
>> I am doing your tutorial of free energy calculations for methane in water.
>> I have created the .mdp  and  .sh files using the perl script you
>> provided.
>> I have also made the FREE_ENERGY and MDP directories as in the job. sh
>> script. gro file and topology files are also in the relevant folder but
>> when I run job.sh script with command bash job.sh, it says the files the
>> .mdp file, the methane_water.gro file and topol.top file either dont exist
>> or not accessible. I have checked the files are in their proper places and
>> are searched on terminal and opened though comand with vi editor. I have
>> also given chmod 777 permission to these files. but no way out of the
>> problem. please help me out. I have been searching the archive and google
>> for the last three days but could not sort out. When i run the grompp and
>> gmx md run commands directly through the terminal it works but not through
>> the job.sh.
>> Please suggest me a solution. Sorry for the long text or for addressing
>> directly to you.
>>
>
> Without specific error messages, I have nothing to go on to suggest a
> solution. Perhaps you should be consulting your system administrator if the
> commands are syntactically valid but not operational in the queued
> environment.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] problem in running job.sh for free energy calculations.

[Mark Abraham]

Hi,

Probably your initial working directory is not what you expect it to be.
That's often supposed to be set in your job script. Check out the
documentation for your cluster or submission system, and then ask the
admins.

Mark

On Mon, Apr 9, 2018, 17:25 neelam wafa  wrote:

> Dear sir Justin
>
> I am doing your tutorial of free energy calculations for methane in water.
> I have created the .mdp  and  .sh files using the perl script you provided.
> I have also made the FREE_ENERGY and MDP directories as in the job. sh
> script. gro file and topology files are also in the relevant folder but
> when I run job.sh script with command bash job.sh, it says the files the
> .mdp file, the methane_water.gro file and topol.top file either dont exist
> or not accessible. I have checked the files are in their proper places and
> are searched on terminal and opened though comand with vi editor. I have
> also given chmod 777 permission to these files. but no way out of the
> problem. please help me out. I have been searching the archive and google
> for the last three days but could not sort out. When i run the grompp and
> gmx md run commands directly through the terminal it works but not through
> the job.sh.
> Please suggest me a solution. Sorry for the long text or for addressing
> directly to you.
>
> Thanks in advance.
>
> Regards
> Neelam wafa
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] problem in running job.sh for free energy calculations.

[Justin Lemkul]

On 4/9/18 11:25 AM, neelam wafa wrote:

Dear sir Justin

I am doing your tutorial of free energy calculations for methane in water.
I have created the .mdp  and  .sh files using the perl script you provided.
I have also made the FREE_ENERGY and MDP directories as in the job. sh
script. gro file and topology files are also in the relevant folder but
when I run job.sh script with command bash job.sh, it says the files the
.mdp file, the methane_water.gro file and topol.top file either dont exist
or not accessible. I have checked the files are in their proper places and
are searched on terminal and opened though comand with vi editor. I have
also given chmod 777 permission to these files. but no way out of the
problem. please help me out. I have been searching the archive and google
for the last three days but could not sort out. When i run the grompp and
gmx md run commands directly through the terminal it works but not through
the job.sh.
Please suggest me a solution. Sorry for the long text or for addressing
directly to you.


Without specific error messages, I have nothing to go on to suggest a 
solution. Perhaps you should be consulting your system administrator if 
the commands are syntactically valid but not operational in the queued 
environment.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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

==

--
Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] problem in running job.sh for free energy calculations.

[neelam wafa]

Dear sir Justin

I am doing your tutorial of free energy calculations for methane in water.
I have created the .mdp  and  .sh files using the perl script you provided.
I have also made the FREE_ENERGY and MDP directories as in the job. sh
script. gro file and topology files are also in the relevant folder but
when I run job.sh script with command bash job.sh, it says the files the
.mdp file, the methane_water.gro file and topol.top file either dont exist
or not accessible. I have checked the files are in their proper places and
are searched on terminal and opened though comand with vi editor. I have
also given chmod 777 permission to these files. but no way out of the
problem. please help me out. I have been searching the archive and google
for the last three days but could not sort out. When i run the grompp and
gmx md run commands directly through the terminal it works but not through
the job.sh.
Please suggest me a solution. Sorry for the long text or for addressing
directly to you.

Thanks in advance.

Regards
Neelam wafa
-- 
Gromacs Users mailing list

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