[gmx-users] a question

[Yuguang Mu]

We have two complied versions of gromacs, one is complied by intel fortran
7.0, one is complied g77

I check different water models,

one is spc, one is tip3p amber model with  1146 water molecules in each
case (with PME cutoff 1.0)

By using the intel fortran versions

for spc such line is printed out
 ***************************************************************
 Going to use C-settle (573 waters)
 wo = 0.888096, wh =0.0559521, wohh = 18.0154,
 rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
 rone = 1, dHH = 0.16333, dOH = 0.1
 ***************************************************************

the average density turns out to be  966

for tip3p such line is printed out
********************************************************
Going to use C-settle (9781 waters)
wo = 0.888099, wh =0.0559503, wohh = 18.016,
rc = 0.075695, ra = 0.00655606 rb = 0.0520322, rc2 = 0.15139,
rone = 1, dHH = 0.15139, dOH = 0.09572
**********************************************************

the average density turns out to be  986
(exactly as the amber sander results)

which mean that it do simulated using different water model.


But when I use g77 version,
no "Going to use C-settle (573 waters)" line appears.
the different water model simulations nearly give the same density:
966 , which turns out that it cannot use correctly the other water model.



Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On 22 Aug 2003, David van der Spoel wrote:

> On Fri, 2003-08-22 at 09:14, Yuguang Mu wrote:
> > In the output log file in some case the following line is printed out
> > (when gromacs is compiled with assembly innerloops)
> > In other cases without assembly innerloops, this didnot print out.
> >
> This should not have any relation to assembly loops or not. Isn't it
> related to using fortran or not?
>
> > I am worried about it, because it seems to effects the density of water.
> Can you be more specific? Give some numbers and simulation details.
>
> >
> > ***************************************************************
> > Going to use C-settle (573 waters)
> > wo = 0.888096, wh =0.0559521, wohh = 18.0154,
> > rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
> > rone = 1, dHH = 0.16333, dOH = 0.1
> > ***************************************************************
> >
> > Dr. Yuguang Mu
> > Institute for Physical and Theoretical Chemistry
> > J.W. Goethe University Frankfurt am Main
> > Marie Curie Str. 11
> > 60439 Frankfurt/Main, Germany
> > Tel: +49-(0)69-798-29711
> >
> >
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
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