Emanuel Peter wrote:
Dear Gromacs-users,
At the moment I have a question which regards the different
electrostatic algorithms mentioned in the Gromacs-manual.
I did some simulations and I tried three different electrostatic
algorithms: Cut-off, Shift and PME.
It is clear to me what Shift and PME means principally, but I ask myself
which electrostatic algorithm is used by Cut-off.
I know that Cut-off means a twin-range-electrostatics calculation with
rlist as the first range and r_coulomb as the second range. Both are
calculated within different frequencies. Is that true ?
In my .log file it is mentioned that when using Cut-off a default value
r_coulombswitch equal to 0 is set. It is the same in the case of
r_vdwswitch.
Does that mean that I use in this special case a switch function which
switches at 0 nm which represents in this case a shift-function that
shifts my electrostatic potential in such a way, that it decays to zero
at r_coulomb?
I think this means that I used a shift-function which is calculated
within the twin-range-electrostatics scheme.
Is this true?
What disadvantages does the twin-range-electrostatics calculation
have in comparison to PME?
Is it true that PME could stabilize my system artificially?
No, it is the other way around. Cut-offs are bad.
Check:
J. Chem. Theor. Comp. 2 pp. 1-11 (2006)
Now another question:
Some people who perform molecular-dynamics calculations are stabilizing
the dihedral angles in the forcefield to avoid 'unrealistical'
fluctuations of their protein. Is this a reasonable way to simulate a
protein?
No, you are changing the force field in that way. I haven't heard of
this previously.
Is it also reasonable to heat up a crystal -.pdb structure, determined
by x-ray, slowly from 50 K up to 300 K in a couple of steps?
Does this have any purpose or is this just a non proven setup of my
structure?
Thanks for your good advice in advance!
Best regards,
Emanuel Peter
Institute of Phys. and Theor. Chemistry
93053 Regensburg
Germany
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
