[gmx-users] Re: constraints problem
wurl04 at iccas.ac.cn
Wed Nov 22 02:49:19 CET 2006
i mean i always met with problems simulating amorphous and crystalline systems without bond constraints, your suggestion of reducing the time step is very reasonable, and i don't know a compressibility of 1e-6 will be suitable for a polyethylene crystal cell?
and i have also not succeeded in simulating such systems with constraints= all-angles, it always makes long warnings during the md process and stop soon. my time step is 1fs, the oplsaa force field, and the version is gromacs3.3 with pme.c updated. do i need to make specific changes to the default run perameters for systems with all angles bonds constraint?
>Rongliang Wu wrote:
>> dear all,
>> thanks for your great suggestions and i have met with new problems in
>> simulation of bulk systems or crystal cells when no constraints are
>> utilized, the systems either explode or met with "segmentation fault"!
>> and i am sure my systems are well minimized.
>> and again when constraints= all-angles, the system often collapse.
>> i have always being using the all-bonds constraints, but the bond length
>> distribution can no be thus derived.
>> the constraint parameters in mdp files are defaults!
>> best regards!
>Please state clearly
>+ what you have tried
>+ if there were problems
>If I read you correctly you want to study bond length distributions, in
>which case you need to turn off constraints and reduce the timestep to
>0.2 and 0.5 fs.
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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