[gmx-users] NPT simulation problems

Dr. Christoph Freudenberger christoph.freudenberger at ch.tum.de
Thu May 13 12:05:13 CEST 2004

David van der Spoel wrote:
> On Thu, 2004-05-13 at 05:39, nicolas Dinter wrote:
>>Dear Gromacs users,
>>I am trying to make a NPT MD simulation with 150 Benzenemethanethiol,
>>alfa-methyl molecules in a 30*30*30 box. After having found the equilibrium,
>>I run the NPT simulation and I had never found the box equilibrium, the size
>>is always decreasing, also after a 300 ps simulation!
>>Maybe the force field parameters are incorrect or the tau_p and tau_t are
>>not well choosen (parameters witch I dont understand how to fit them).
>>If somebody could help me it will be very nice. Thank you.
> Check the density from g_energy and compare to experimental value. Do
> also check energy and pressure.

Be aware that the box length is measured in nm not Angstroem. I'd expect
your box vectors to be in the 3nm range for 150 molecules rather than 30nm.

Dr. Christoph Freudenberger
Lehrstuhl für Organische Chemie II
Department für Chemie
Technische Universität München

Lichtenberg Straße 4
85747 Garching

Tel.: ++49 (0)89 289 13313
Fax.: ++49 (0)89 289 13210
email: Christoph.Freudenberger at ch.tum.de

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