[gmx-users] Re: Question about CCl4 box!

David spoel at xray.bmc.uu.se
Sat May 3 15:25:01 CEST 2003

On Sat, 2003-05-03 at 14:40, PeiQuan Chen wrote:
> Dear gmx-users:
> >Alternatively you can leave out one of the constraints. You will still
> >get the same geometry, since the constraint problem is completely
> >determined by 9 inequalities. You can leave out any of the 10
> >constraints
>    I have leaver out one of the constraints( 4 5 ).
>    Now that I can reproduce the exp data of density and DHvap
>    Density: exp.(1.594) cacul.(1.572)
>    DHvap:   exp.(32.54kJ/mol ) cacul.( 32.38kJ/mol)
>    But I can't still the make the tau_p value more smaller.If I make the value smaller.
> The problem is the same as I have report.
>    I want to ask how to change the tau_p smaller and the simulation doesn't carsh. 

OK, that looks good, experimental values reproduced within 1%. If you
really want a shorter tau_p you probably need a larger box. Shorter
tau_p means smaller pressure fluctuations, but larger box fluctuations.
This is probably why your runs crash, because box < 2 cutoff.

However, if you do a run of 1 ns or so, you'll probably see that your
average pressure is correct, and that is what matters I'd say.
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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