João M. Damas wrote:
What do you mean by mutually inconsistent? From what I understand, they
aren't.
I mean a set for which there is no molecular arrangement that satisfies.
Also, [bonds] type 6 won't work for what I want, since I don't want to
keep the molecules at a fixed distance but to prevent them from coming
closer, i.e. I want a potential that depends on the distance between the
atoms.
Testing the distance restraints can be quite exhaustive when you have
about 160 restraints, and I am considering just the test case I'm
trying, not the actual system which will have some more organic
molecules, which will lead to a greater amount of combination of
restraints...
#ifdef is your friend here...
[ distance_restraints ]
<set to test now >
#ifdef BLAHBLAH
<set to test later>
#endif
Now you just move the #ifdef to rearrange your test cases.
I might start with an even smaller test case until you prove you can
deal with both the input formatting issues and the physics issues with
it. Testing will be faster, for starters.
Mark
On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
João M. Damas wrote:
Gromacs users,
I have a small test system of about 2500 atoms which consists on
a few organic molecules in a box of water. I'm trying to use
distance restraints to keep each molecule apart from each other
and I've failed until now.
I'll start by saying that the simulation runs smoothly without
using distance restraints and that I've created a single
molecule topology that describes all organic molecules, allowing
the use of distance restraints. By applying just one distance
restraint between two atoms of different molecules, the
simulation still runs without problems. When I apply all the
distance restraints I want, the system crashes in the first few
steps with an XTC error, which is preceded by a few inconsistent
shifts and some LINCS warnings. Varying the number of restraints
that I use, makes the crash happen at later steps (500ish),
meanwhile giving a lot of inconsistent shifts before crashing
with a fatal error: Number of grid cells is zero. I know it
seems I'm experimenting blindly, but varying the number of
restraints was the first that occurred to me.
I've searched the list for similar problems and tried a few more
tests. I've turned off LINCS and reduced the time step and it
didn't solve the problem, the box blew up after a few steps due
to pressure problems. Since it could be a PBC problem, I tried
to increase the size of the box, but it didn't solve the
problem. Turning of PBC did solve the problem, but I really need
PBC. I've also changed the low, up1 and up2 to values inferior
to half the box size (I don't even care about the up1 and up2
values in this application, and I was setting them to 5.0 nm
before), but it didn't solve the problem either. I'm a little on
a dead end here and I was hoping anyone could give me some insight.
By the way, I'm using GROMACS 4.
The simplest explanation is that your sets of distance restraints
are mutually inconsistent. This destabilizes the system and
eventually leads to your symptoms. Consider using [bonds] type 6,
per advice of manual section 4.3.4. Either way, if you add these
restraints one by one after testing that the previous set seemed to
work OK (didn't crash, trajectory looks right), you may uncover your
issue.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
------------------------------------------------------------------------
_______________________________________________
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
_______________________________________________
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
