[gmx-users] energy

jayant james jayant.james at gmail.com
Mon Apr 6 18:19:09 CEST 2009

Thanks for your mail. I used two different operating systems and in both I
found this problem of the energy file recurring!!
Well I will go ahead and use the tpdconv to extend the simulations.
On Sun, Apr 5, 2009 at 4:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> jayant james wrote:
>> Hi!
>> I ran a simulation for 1ns and I find that the energy file has been
>> written only till 627 ps. I am wondering how to extend my simulations  as I
>> need the energy file (simulated with 1bar pressure)!!!
>> I wonder why this is happening on a consistent basis. I cannot think of
>> the energy file being large nor the operating system not being able to write
>> it, because the .trr file is much larger than this file and is being written
>> down succedfully till 1000ps.  I am using GMX 4.0.
>> I welcome any suggestions on how to extend the MD run and to overcome this
>> energy file problem.
> You should be running version 4.0.4, and either way using checkpoints for
> your restarts. There's no GROMACS-related reason why your energy file should
> stop being written. It's rather more likely you or your filesystem have done
> something to cause the observations, but we can't tell what on this
> information.
> Mark
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Jayasundar Jayant James

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