Re: [gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Mark Abraham]

Hi,

Justin suggested confirming with gmx check. Since we know the file is
large, find out what your file system is, or try another machine.

Mark

On Mon, 23 May 2016 10:50 Antara mazumdar  wrote:

> Dear Mark,
>
>I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
> system. What further could be done?
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
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[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Antara mazumdar]

Dear Mark,

   I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
system. What further could be done?
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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Re: [gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Justin Lemkul]

On 5/21/16 9:47 AM, Antara mazumdar wrote:

Dear Sir,

The MD.trr i expect to be having 382ns of data as is mentioned in the log
file and MD.xtc that was generated alongwith MD.trr when the simulation
ran  has 382ns.

However, MD.trr has problems in giving output beyond 25ns. Could it be
corruption of frames or something?


gmx check will tell you this.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Antara mazumdar]

Dear Sir,

The MD.trr i expect to be having 382ns of data as is mentioned in the log
file and MD.xtc that was generated alongwith MD.trr when the simulation
ran  has 382ns.

However, MD.trr has problems in giving output beyond 25ns. Could it be
corruption of frames or something?
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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