On 5/6/15 7:26 AM, Mark Abraham wrote:
On Wed, May 6, 2015 at 9:01 AM Seyed Mojtaba Rezaei Sani <
s.m.rezaeis...@gmail.com> wrote:
Dear Justin
Thanks for your kind response. I didn't notice the point you mentioned. It
seems that grompp doesn't care the difference betwen vdwq and vdw-q.
however, I corrected the script. The error remains even in the case of
choosing 2 nodes. The only way to have a successful run is a serial
calculation.
Then that's life (except that if your protein is non-spheroidal, you might
have better luck with the long axis aligned to the z-axis).
The domain decomposition code expects bonded interactions to be of shorter
range than short-ranged non-bonded interactions, so will not produce a
decomposition that has a bonded interaction that starts in one domain,
crosses another domain, leaves by the opposite face, and reaches a third
domain. This is implemented by setting a minimum size for domains based on
many properties of the observed starting structure. There's a brief summary
of these choices printed in every .log file.
The use of couple-intramol triggers the generation of atypical
interactions, that are implemented like bonds as far as the DD code knows,
and for a protein those "bonds" are so much longer that they set a minimum
size that means a decomposition is infeasible.
AFAIK, FEP on a whole protein isn't going to work at all anyway.
True. But is "DOX" isn't a protein; it's doxorubicin. There is no reason that
I can think of that would cause DD to fail unless the box is unreasonably small.
An extension of normal interactions out to 1.9 nm should be within normal
limits if the box is of adequate size. Perhaps the OP can give us more
information (linking the .log rather than trying to attach it) and describing
the box size.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
