[gmx-users] box of methanol

Luca Monticelli luca.monticelli at unimi.it
Thu Jul 25 16:14:52 CEST 2002

Hi all,

finally I found some time to run a
couple of tests on a box of methanol,
generated with the method suggested by

I used the G43a1 force field, with
cut-offs 0.8/1.4 (Gromos-96 was
parameterized with these twin-range
cut-offs, right?) and NPT conditions;
box size is approximately 4.3*4.3*4.3,
timestep=2fs, nstlist=5, no constraints,
compressibility= 4.575e-4; total time is
5 ns.

These are the results.
It takes ~500 ps for the pressure to 
become relatively stable.
Excluding the initial 500 ps, the 
average d=749, with
an RMSD of 3.9.

If I change the cut-offs to 0.9/1.4, 
leaving all other
parameters identical, I find d=782, with
an RMSD of 3.5. Not bad, the error is 
only ~1.1%.

Now I am running a couple of tests to check
for dependency on the box size; I 
already run 1 ns on a smaller box (about 
3*3*3), and the results seem to be very 
similar, so far.

If anybody is interested in using this 
box, just let me know.


Luca Monticelli
Centre for bio-molecular
Interdisciplinary Studies
and Industrial applications
University of Milan, Italy
Istituto di Chimica del Riconoscimento
C.N.R., Milano, Italia
e-mail: luca.monticelli at unimi.it
phone: +39 02 2850 0031
fax:   +39 02 2850 0036

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