[gmx-users] Calculate interaction energy dynamically

[Justin Lemkul]

On 7/23/13 1:54 PM, Davit Hakobyan wrote:
> Thank you very much for your continuous support.
>
>> Date: Tue, 23 Jul 2013 12:06:57 -0400
>> From: jalemkul at vt.edu
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>>
>>
>>
>> On 7/23/13 11:05 AM, Davit Hakobyan wrote:
>>> Thanks so much for the suggestion.
>>>
>>> By using the command:
>>>
>>> trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr
>>>
>>> the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm).
>>>
>>> Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the "rerun" flag:
>>>
>>> mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr  -c system_ordered.gro  -e system_ordered.edr
>>>
>>> many warnings were shown like:
>>>
>>> WARNING: there may be something wrong with energy file system_ordered.edr
>>> Found: step=-1, nre=68, nblock=0, time=31000.
>>> Trying to skip frame expect a crash though
>>>
>>> WARNING: there may be something wrong with energy file system_ordered.edr
>>> Found: step=-1, nre=68, nblock=0, time=32000.
>>> Trying to skip frame expect a crash though
>>>
>>> WARNING: there may be something wrong with energy file system_ordered.edr
>>> Found: step=-1, nre=68, nblock=0, time=33000.
>>> Trying to skip frame expect a crash though
>>>
>>> Do these warnings point to some error?
>>>
>>
>> Where do they come from - mdrun? g_energy? gmxcheck?  If you haven't run
>> gmxcheck on the .edr file, please do.
>>
>
> The above warnings are issued by mdrun. The g_energy generates similar warnings like:
>
> WARNING: there may be something wrong with energy file system_ordered.edr
> Found: step=-1, nre=68, nblock=0, time=74000.
> Trying to skip frame expect a crash though
>
> WARNING: there may be something wrong with energy file system_ordered.edr
> Found: step=-1, nre=68, nblock=0, time=75000.
> Trying to skip frame expect a crash though
> Last energy frame read 75 time 75000.000
> ...
>
> The gmxcheck command:
>
> gmxcheck -f system_ordered.trr -c system_ordered.tpr -n system_ordered.ndx -e system_ordered.edr
>
> does not give any warning/error.
>

Can you please provide the actual gmxcheck output?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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