[gmx-users] walls...still struggling (not)
feenstra at chem.vu.nl
Mon Dec 1 08:51:03 CET 2003
David van der Spoel wrote:
> On Mon, 2003-11-24 at 10:52, Sherwin J. Singer wrote:
>>I can report 1) a problem solved, and 2) unexpected behavior
>>concerning genbox input options.
>>1) I've written recently about constructing flexible silanol groups on
>>an otherwise frozen silicate wall. Gromacs md would move the silanol
>>oxygens and hydrogens, but would claim the kinetic energy was zero,
>>gave "nan" for the number of degrees of freedom, and would not
>>thermostat or energy minimize the structure.
>>My problem turned out to be the center of mass constraints. I had
>>given the two groups for center of mass removal as "comm_grps = WALL1
>>WALL2", where the WALL1 group is frozen, and WALL2 is the silanols.
>>When I simply specify "comm_grps = SYSTEM", all is well. I'm not sure
>>why removing 3 center of mass degree of freedom among 448 silanol
>>atoms messed me up, but it did.
> thanks for the report.
>>2) I then went to solvate my wall.
>>"genbox -cp walls_run1.gro -p walls.top" added 0 waters, while
>>"genbox -cp walls_run1.gro -cs spc216.gro -p walls.top" added 9180
>>waters. Isn't spc216.gro the default for the -cs option?
> yes, but you still have to give the -cs option, otherwise the behaviour
> of the program is different.
I.e., adding solvent is optional, controlled by specifying -cs (or not),
and spc216.gro is the default.
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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