[gmx-users] gromacs 4.6.4 version - nvt equilibration error

[Justin Lemkul]

On 11/19/13 9:01 AM, MUSYOKA THOMMAS wrote:
> Hi Vsharma
> Try this mdrun -v -deffnm nvt

That's exactly what the command was.  The command itself is not the problem.

I have seen disk space errors come up under two circumstances not actually 
related to disk space: (1) file system blips and (2) crashes.  Is the error 
reproducible?  That is, did it happen once or multiple times?  If the former, 
it's probably just a file system blip.  If the latter, does it happen at the 
same step in the simulation each time?  Does the simulation run for a while and 
produce any other useful diagnostic output to the .log file or stderr that 
indicates a crash?

-Justin

> cheers
>
>
> On Tue, Nov 19, 2013 at 3:42 PM, <vsharma at imtech.res.in> wrote:
>
>>
>>
>> hell all ..
>>
>> i am trying to simulate 414 aa long protein
>>
>> i am getting following error on giving command for NVT equilibrations:
>> COMMAND : MDRUN -DEFFNM NVT -V
>>
>> ERROR:
>> File input/output error:
>> Cannot write trajectory frame; maybe you are out of disk space?
>>
>> i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB
>> Disk space, i am simulating 414aa long protein for 10ns.
>>
>> i have confirmed working status for my parameter files as with gromacs
>> 4.5.5, dynamics are working properly.
>>
>> i doubt, if there are some issues with gromacs 4.6.4 version
>>
>> any help
>>
>> --
>> VANDNA
>> JRF
>> C/O Dr. Girish Sahni
>> Protein Science lab
>> Phone No. 0172-2690830
>> Institurte of Microbial Technology (IMTech)
>> Sector -39A, Chandigarh,160036
>>
>> --
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-- 
==================================================

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

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