[gmx-users] GROMOS vs. GROMACS
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Thu Feb 28 17:17:48 CET 2002
The simulations with the different timesteps are done. I got the results
if(dt==1fs) after some step:
+pressure scaling more than 1%
+water molecule starting at atome 2681 can not be settled
if(dt=4fs) shake error at step ...
> 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
> Groeten, David.
> 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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