vivek sharma wrote:
Hi Tehre,
i am running a job by keeping a part of molecule freeze ....by using the
.mdp option....
What is your entire .mdp file?
-Justin
______________
________
energygrps_excl = Terminal Terminal Terminal SOL ! To remove
computation of nonbonding interactions between the frozen groups with each other
and surroundings (i.e. the solvent, SOL)
freezegrps = Terminal ! Index group to freeze
freezedim = Y Y Y
! Freeze this group in all directions, x,
y, and z
___________________________________________________
where frreze is a group mentioned in the index file...
During the run the job is being terminated with the following error
.
__________________________________________________________
Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22
-3.51079e+22 -3.51079e+22
-------------------------------------------------------
Program mdrun_d, VERSION 3.3.3
Source code file: ns.c, line: 258
Fatal error:
Box was shifted at least 10 times. Please see log-file.
-------------------------------------------------------
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 0 out of 24
srun: error: n216: task0: Aborted
srun: Terminating job
__________________________________________________________________
Can somebody give an insight in the problem for figuring out the
probable cause of the error.
PS::Before the run I mentioned the boxsize in editconf as "-box 7.5 5 6
", to keep the size of box and number of solvent optimum.
Does it have anything to do with the mentioned error ?
Looking for suggestions..
with thanks,
Vivek
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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