<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi,<br><br>I tried to run on single node now. Now the error is different saying<br>"One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off"<br><br>This means that my box shrinks during dynamics (this is not constant volume MD) But when Solvent is present in the same system, this does not happen. How should i deal with it then ?<br><br>Regards,<br>Nikhil<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, 8 October, 2009 11:57:46 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Load imbalance and Y size error<br></font><br>nikhil damle wrote:<br>> Hi all<br>> <br>> I am trying to simulate a system of 3168 atoms in vacuum in PBC box (-d=0.9 nm). Since there are no solvent molecules, i am unable to neutralise the system using addition of ions (Hence system has +3 charge). As soon as i start the MD run after putting the whole system in box, there is imbalanced force of 80% due to which right in the beginning, dynamic load balancing is turned on. But even after this, there is ~22% loss of performance and after certain steps MD crashes saying :-<br>> <br>> "Fatal error: The Y-size of the box (4.618413) times the triclinic skew factor (0.866051) is smaller than
the number of DD cells (2) times the smallest allowed cell size(2.000000)"<br>> <br>> Can anyone explain the origin of this error and how to deal with it ?<br><br>Try running with one processor to see if it's your system or the domain decomposition algorithm that is the problem. DD doesn't necessarily cope well with highly heterogeneous distributions of particles.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a
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