[gmx-users] rerun warning

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hi Justin,
> 
> As I dont have velocities defined in my traj. file, please can I know if theres some possibility of  including them to the traj. file
> 

If you're re-running from a .xtc file, then no, there is no way to store 
velocities in such a file.  You need a .trr if you need to calculate anything 
related to velocities.

-Justin

> 
> cheers,
> chetan 
> 
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: 16 September 2010 12:35
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] rerun warning
> 
> Poojari, Chetan wrote:
>> 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...
>>
> 
> You need velocities, and thus, a .trr file.
> 
> -Justin
> 
>> cheers,
>> chetan
>> ________________________________________
>> 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.
>>
>> Mark
>>
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> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================