[gmx-users] rerun warning

Poojari, Chetan c.poojari at fz-juelich.de
Thu Sep 16 12:33:33 CEST 2010

Hello Mark,

Thank you very much for quick reply.

I am looking for LJ and coul interactions, please can i know what can be done to avoid these warnings if incase i want to calculate kinetic quantities...

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [mark.abraham at anu.edu.au]
Sent: 16 September 2010 12:12
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] rerun warning

----- Original Message -----
From: "Poojari, Chetan" <c.poojari at fz-juelich.de>
Date: Thursday, September 16, 2010 20:04
Subject: [gmx-users] rerun warning
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>

> Hi,
> I am doing  rerun to calculate  LJ-SR & coul-SR
> interactions and  other energy terms for energygrps defined
> in mdp file.
> I have constrained all bonds with lincs algorithm in mdp file.
> While running rerun i get following warnings........
> WARNING: Some frames do not contain velocities.
>          Ekin,
> temperature and pressure are incorrect,
>          the virial will
> be incorrect when constraints are present.
> Please can I Know if the energy values generated are they
> incorrect........if so how can i recalculate correct energies as
> i dont have velocities in my file to use  g_traj

If you're not trying to calculate the kinds of *kinetic* quantities described in the warning, then you don't care. Your first sentence sounds like you're after *static* quantities. If you do want kinetic quantities, then you're in trouble.


Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

More information about the gromacs.org_gmx-users mailing list