[gmx-users] Problems Running Gromacs v-5.0.4

Stephen P. Molnar s.molnar at sbcglobal.net
Sat Feb 28 01:25:20 CET 2015

Thank you for your reply.

Stephen P. Molnar, Ph.D.                                    Life is a fuzzy
Foundation for Chemistry                                   Stochastic and
(614)312-7528 (c)
Skype:  smolnar1

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
Justin Lemkul
Sent: Friday, February 27, 2015 5:50 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problems Running Gromacs v-5.0.4

On 2/27/15 4:01 PM, Stephen P. Molnar wrote:
> The original of this message was sent on 2/18.  To date it has greeted 
> freeted with thundering silence.  I would really appreciate an answer, 
> even if no solution is readily apparent.
>> I have compiled and installed Gromacs v-5.0.4 (rather than using the 
>> version bundled with the distribution() in RoboLinux 7.81. without 
>> any warning or error messages.
>> However, I have encountered problems running gmxdemo.  Although I get 
>> the message "Display variable is set" I see a flash, but the window 
>> does not stay open.  However, I do get the final display of the box 
>> and the simulation.

Probably my first question is how are you running gmxdemo?  It was removed
from the source code in 2012...before version even the release of 4.6-beta1.

>> The second problem probably involves permissions.  If I run the demo 
>> as the superuser, (RoboLinux does not allow the enablement of the 
>> root during the installation) The demo runs to completion without 
>> problems, other that the one of the vanishing window.
>> Running gmxdemo as the superuser generated 39 files (including 
>> gmxdemo and cpeptide.pdb) while running as a user generates 23 files.

Depends on where GROMACS is installed and what you've done to get gmxdemo
running.  FWIW, it was removed because it wasn't useful and no one wanted to
maintain it.  If it's not working, the solution is to find better tutorial
material, as suggested in README.tutor :)



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

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