[gmx-users] Free energy calculation, Methane in water tutorial

Justin Lemkul jalemkul at vt.edu
Fri Sep 2 16:31:43 CEST 2016

On 9/2/16 9:53 AM, sun.iba2 wrote:
> Yes. But nothing else is printed on screen. Log files are creared but incomplete. When I used perl script to generate respective .mdp files for mininization and equilibrium, i found all of the generated files for 21 lambda values were empty. However when I tried with my molecule, the 21 .mdp files are created properly but still encountered same error with my file i.e. .tpr file is missing.

This suggests something at the very top level is not set up correctly (paths, 
environment variables, etc).  Run the commands in the job script interactively 
to figure out which step is failing.


> <div>-------- Original message --------</div><div>From: Justin Lemkul <jalemkul at vt.edu> </div><div>Date:02/09/2016  4:57 PM  (GMT+05:30) </div><div>To: gmx-users at gromacs.org </div><div>Cc:  </div><div>Subject: Re: [gmx-users] Free energy calculation, Methane in water tutorial </div><div>
> </div>
> On 9/2/16 7:09 AM, Sun Iba wrote:
>> Hello dear users
>> I am following Justin's tutorial for free energy calculation of Methane in
>> water. I have downloaded the job.sh file and trying to run it in terminal
>> using: sh job.sh but it is giving following error:
>> Program mdrun, VERSION 5.0
>> Source code file:
>> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
>> Can not open file:
>> min0.tpr
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> Please help me with error.
> grompp failed to produce the .tpr file.  Use the screen output to figure out why.
> -Justin


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list