[gmx-users] GROMOS vs. GROMACS
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 28 16:22:54 CET 2002
On Thu, 28 Feb 2002, Nguyen Hoang Phuong wrote:
>The GROMOS and GROMACS are used to simulate the same system of a peptide
>in water. The force field 43A1 are employed. The same input parameters
>(in the mdp file) are used. However, the temperature is
>shifted if GROMACS is used and I get the right temperature if GROMOS is
>Does anyone has the experience with this problem?
I recall we tested this once. It seems there is an artefact with due to
the timestep in GROMOS leading to cancellation of errors. Could you rerun
the tests with a shorter and with a longer timestep? If you used 2 fs
before, please redo it with 1 fs and 4 fs.
In GROMACS there definitely is some lag due to the fact that we use the
velocities from the previous timestep for scaling.
The real solution is to use PME, because that takes the source of the
heating (the cut-off) away
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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