On 11/1/12 4:56 PM, Alex Marshall wrote:
I've created a position restraint file for the specific waters that I need
to immobilize, but I'm having a hard time getting grompp to apply it
successfully. No matter where I put #include "posre.itp" in my topology
file grompp returns fatal errors about the atomic indices being out of
bounds. Is it actually possible to only apply position restraints to some
molecules within a species and leave the rest alone?
Yes, but you can't simply #include "spc.itp" and then call the position
restraint file, for example. You need a [moleculetype] for the entire block of
water, since position restraints can only be applied per [moleculetype].
-Justin
On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/31/12 3:55 PM, Alex Marshall wrote:
Chris, is that for freeze groups or position restraints?
I will assume Chris was referring to the restraint method - you need an
index file for creating the position restraint .itp file using genrestr.
It will save you a ton of time over doing it manually.
-Justin
On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:
No need to rename... just make an .ndx group.
-- original message --
As I understand it, position restraints for an atom are set in the
topology
file and applied to that atom in each of that species. In order to
restrain
some but not all of the water I'd have to copy the topology of my water
model and add the restraints, then rename (and group together) the atoms
I
want to freeze so that they're identified with the appropriate topology
file. Does this sound like it would work? Is there some other way that
you
might do it?
Thanks
On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall <amarsh59 at uwo.ca>
wrote:
Justin: I'll try using position restraints instead of freezing the water
in the tube. Thanks for the tip.
Bogdan: I don't think I'm using constraints other than freeze groups. I
wasn't using energy group exclusions though. I tried running the
simulation
from the same initial configuration with newly-defined energy groups
CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second
for
the free atoms. The list of exclusions reads:
energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN
Long story short, I'm roughly 15 ns into the simulation and the same two
waters have jumped. I'll check the manual again though. Thanks.
On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu <bcostescu at
gmail.com>wrote:
On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall <amarsh59 at uwo.ca>
wrote:
Thanks Justin. I identified the offending waters using vmd (adding 1
to
resID and atom number since vmd starts counting at 0) and checked
confout.gro to make sure the coordinates matched up. I only have one
group
for all frozen atoms in the system, and these guys are definitely in
it.
Are you using some kind of constraints ? Are you using energy group
exclusions to avoid interactions between frozen atoms ? If you search
the manual for "frozen" you'll find some warnings and recommendations.
Cheers,
Bogdan
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Virginia Tech
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