servaas michielssens wrote:
Thanks for your help, I checked the perl script (amb2gmx.pl) it should
work for a solvated protein. The solvend and box are converted to
gromacs but the box information is not converted as it should, amber
only defines d and 3 angels (+information in the topology that it deals
with a truncated octahedron), while gromacs needs 3 vectors to defines a
truncated octahedron and this information is only in the .gro file not
in the topology. The amb2gmx.pl script only copies tree values to the
.gro file for an truncated octahedron so gromacs thinks it is a cubic box.
Normally the ensembles are both NTP, I can hardly believe that
differnces in algoritm would cause a "Constraint error in algorithm
Lincs at step 0" and make the simulation crash.
Well, possibly not *if* the only material difference was the
implementation of fixed-pressure, but as we've discussed, you've
probably got several material differences in the algorithms that shift
your equilibrium ensemble. Still, if your box was that wrong, then
there's no surprise about a LINCS error.
But I agree that this
procedure is not the way to go for a good simulation, the only intention
of this was doing a speed comparision.
Still gotta compare apples with apples, unless you're trying for a
pre-determined conclusion :-)
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
