I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? What I am trying to ask is, does GROMACS consider these as 2 different atoms placed at the respective positions or do the 2 atoms overlap?
What could be the reason for the segmentation fault? Is it because the atoms are too close to each other?
-
Karamyog.
On 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
David van der Spoel wrote:
> Gale, Ella wrote:
>
>>
>> Thanks for the advice, but my force-field has no charges and hence no
>> coulomb potential, so I want the atoms to interact with itself via the
>> Van der Waals functions. I'm using 3.2.1 at the moment and there is no
>> option to use any of the Ewald summation techniques. Is this something
>> that has been added in the most recent version?
>
> Ewald variant are only for Coulomb so far. You can use a normal cutoff
> or a shifted cutoff.
One or two of the early PME papers describe implementation details for
LJ PME, but I am not immediately aware of a modern MD code that
implements it. If you want it, shop around.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
