[gmx-users] Three-site model for acetonitrile

[David]

On Tue, 2003-02-25 at 17:43, Christoph Freudenberger wrote:
> Hi David,
> 
> Thanks for your help so far. Before we continue on that issue I'd like to ask,
> if this is getting to specific for the group and if we should
> continue our disccusion via email.
> AFAIC setting up solvent topolgies and importing parameters from the
> literature is of general interest for gromacs users.
Writing topologies os good for everyone...
> The MD has been running overnight without errors. The results look
> quite good. I have 1ns of the converged solvent box in NPT at
> 300K/1bar:
> 
> Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                  -30.0018   0.201429          0 0.00278205    2.78206
> Density (SI)                731.741    2.57664    2.57525 -0.000293333  -0.293334
> 
> The density is too smal, but the potential energy looks good, isn't it?
> (You posted DHvap=32.94 kJ/mol.)
How far off is the density? Of course it's not your force field... What
do they say in the reference where you got the parameters from. If the
density is too low (and you haven't already done it) you can turn on
dispcorr is enerpres (you should anyway)

> Should I do an md in NVT to have better comparable values? DH corresonds to
> constant volume and temperature AFAIR my physchem lectures...
Isn't DH = U + pV?
pV you get directly from the simulation (check units though), but this
is virtually constant.

> 
> I'm just thinking about a different constrained topology to avoid the error from
> redistributing the mass of the dummie:
> 
> something like:
> [ constraints ]
> ;  ai  aj funct           b0
>     1   3       1          0.26200
>     1   2       1          0.14600
>     2   3       1          0.11600
> 
> Would that work also?
Probably not... The constraints (and bonds) can only exert forces along
the bonds, and hence it is rather ineffecient/impossible to move the
central carbon back on the bond once it moves off there...


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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