Quoting [EMAIL PROTECTED]:
> Hi,
>
> The full mdrun output when the simulation blows up is:
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 6 and 7) rms inf
> bonds that rotated more than 30 degrees:
> .
> .
>
Hi,
The full mdrun output when the simulation blows up is:
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 6 and 7) rms inf
bonds that rotated more than 30 degrees:
.
.
.
Warning: 1-4 interaction between 1 and 6 at d
[EMAIL PROTECTED] wrote:
Hi,
I tried using no temperature coupling and no constraints, that did not
help.
If I run the simulation without the position restraints it works OK.
OK, so they're (interacting with something else to be) generating a
numerical problem.
Could there by something w
Did your minimization converge to a nice, negative potential energy? Also, what
is the full mdrun output when the simulation blows up? You've quoted the last
bit, but it would be more informative to see the whole output, or at least a
description of it (i.e., LINCS warnings).
-Justin
Quoting [
Hi,
I tried using no temperature coupling and no constraints, that did not help.
If I run the simulation without the position restraints it works OK.
Could there by something wrong with the posre file (I'll attach it at
the end of the email).
I want one of the atoms in the lipid to stay in one
[EMAIL PROTECTED] wrote:
Please generate replies to the mailing list sensibly. It's very hard to
work out who you are quoting where in this email. It'd be easy just to
ignore it, and that's the last thing you should want.
Hello,
I'm trying to run a simulation with one lipid molecule in a fi
Hello,
I'm trying to run a simulation with one lipid molecule in a fixed
simulation box without pbc.
I set position restraints on one of the atoms and I seem to keep on
getting the following error:
"...This usually means your system is exploding..."
Do you have any idea what may cause this prob
Quoting [EMAIL PROTECTED]:
> Hello,
>
> I'm trying to run a simulation with one lipid molecule in a fixed
> simulation box without pbc.
> I set position restraints on one of the atoms and I seem to keep on
> getting the following error:
>
> "...This usually means your system is exploding..."
>
> D
Hello,
I'm trying to run a simulation with one lipid molecule in a fixed
simulation box without pbc.
I set position restraints on one of the atoms and I seem to keep on
getting the following error:
"...This usually means your system is exploding..."
Do you have any idea what may cause this
Stéphane Téletchéa wrote:
toma0052 a écrit :
Hello,
I am looking to add position restraints to some atoms of a lipid
bilayer. There seem to be a lot in the list archives on this subject,
but I
am still a tad confused. What I would like to do is to position
restrain the
phosphorus atoms
toma0052 a écrit :
Hello,
I am looking to add position restraints to some atoms of a lipid
bilayer. There seem to be a lot in the list archives on this subject, but I
am still a tad confused. What I would like to do is to position restrain the
phosphorus atoms in only one leaflet of the bi
toma0052 wrote:
Hello,
I am looking to add position restraints to some atoms of a lipid
bilayer. There seem to be a lot in the list archives on this subject, but I
am still a tad confused. What I would like to do is to position restrain the
phosphorus atoms in only one leaflet of the bilay
Hello,
I am looking to add position restraints to some atoms of a lipid
bilayer. There seem to be a lot in the list archives on this subject, but I
am still a tad confused. What I would like to do is to position restrain the
phosphorus atoms in only one leaflet of the bilayer. So how do I g
Philip Shushkov wrote:
Dear Mark,
I have checked this possibility and it turned out that the positional
restraints and constraints did not lead to MD instabilities when run in
serial mode. Unfortunately, the system is pretty large (it consists of
27255 atoms) so it runs quite slowly in serial
Dear Mark,
I have checked this possibility and it turned out that the positional
restraints and constraints did not lead to MD instabilities when run in
serial mode. Unfortunately, the system is pretty large (it consists of 27255
atoms) so it runs quite slowly in serial mode. That is why, I do wan
Philip Shushkov wrote:
Dear GMX-USERS,
I would like to ask you for some advice because I have serious problem
in setting up a PR MD in GROMACS of DPPC monolayer. Prior to actual MD
simulation I have done exhaustive energy minimization up to 10 kJ/mol*nm
convergence criterion. Firstly, I minim
Dear GMX-USERS,
I would like to ask you for some advice because I have serious problem in
setting up a PR MD in GROMACS of DPPC monolayer. Prior to actual MD
simulation I have done exhaustive energy minimization up to 10 kJ/mol*nm
convergence criterion. Firstly, I minimized the system with restrai
things being changed and there might be bugs.
Berk.
From: "Zhou Bo" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To:
Subject: [gmx-users] position restraints with npt ensemble
Date: Thu, 20 Dec 2007 21:21:49 +0800
Hi gmx-users,
I want to restrain some at
Hi gmx-users,
I want to restrain some atoms of a certain protein in water for production,
but I am not sure whether it makes sense to make NPT simulations with
position restraints. I mean if the coordinates of the restrained atoms are
not scaled, it would be problematic in pressure coupling. Thank
Alan Dodd wrote:
Interestingly, merging the peptide chains to one
results in PR working fine. Smells like a bug to
me... but I guess that's the price of using an old
version.
We have done PR MD applied on peptides (40) separated
from each other by water molecules and everything went
fine an
Interestingly, merging the peptide chains to one
results in PR working fine. Smells like a bug to
me... but I guess that's the price of using an old
version.
--- Steffen Wolf <[EMAIL PROTECTED]> wrote:
> Yes, so it looks that minimization ended at a
> metastable point, which
> was surmounted by
Interesting idea, but multiple different start points
have failed with PR, and succeeded with normal MD.
Freeze groups seem to be working OK, so I'm using that
for now - after all, it doesn't need to be 'real', I
just want to equilibrate the lipid/solvent without
moving my carefully-placed peptide
Alan Dodd wrote:
No, minimisation was without PR. Surely minimisation
with PR would *increase* bad contacts, rather than
removing them? I've tried running for a while under
normal MD, successfully and without LINCS errors, then
taking the endpoint and running under PR, but it still
crashes almo
No, minimisation was without PR. Surely minimisation
with PR would *increase* bad contacts, rather than
removing them? I've tried running for a while under
normal MD, successfully and without LINCS errors, then
taking the endpoint and running under PR, but it still
crashes almost instantaneously,
Hi Alan,
well, no, position restraints (and your definition) seem to be fine, and
they work well with my protein/membrane system. Sounds more like your
system is still not well minimized. Using the freezegroup option is not
such a good way, because it will not work well together with the
press
Hello,
I'm trying to run position restraints on multiple
peptides in a protein/bilayer/water system. MD
*without* position restraints runs absolutely fine,
but as soon as I stick that "define = -DPOSRES" in,
some of the molecules explode within a matter of fs.
Any idea why this might be? Is MD w
I used 'genpr' to generate the 'posre.itp' file as I did
many other times
to restrain the entire protein leaving the solvent free.
Once I run 'grompp' I get the following message:
"Fatal error: [ file "1_Cter.top", line 7895 ]:
Atom index (152) in position_restraints out of bounds
(1-3)"
w
Dear Gromacs users,
I need to apply a position restrain to some residues of my protein
leaving the others free to move.
I used 'genpr' to generate the 'posre.itp' file as I did many other times
to restrain the entire protein leaving the solvent free.
Once I run 'grompp' I get the following messa
David Mobley wrote:
David,
OK, I am running MD using position restraints, and I don't get a
separate energy output for "restraint energy" or some such; as far as
I can tell the energy of the restraints is grouped in with the total
potential energy and never reported separately. I would like it t
David,
OK, I am running MD using position restraints, and I don't get a
separate energy output for "restraint energy" or some such; as far as
I can tell the energy of the restraints is grouped in with the total
potential energy and never reported separately. I would like it to be
reported separat
David Mobley wrote:
Dear all,
I'm trying to figure out if there is currently a way to calculate the
position restraint energy (for example, if I'm using a posre.itp file
to harmonically restrain some atoms) on the fly. Can anyone give me
some pointers? I haven't turned up anything useful on thi
Dear all,
I'm trying to figure out if there is currently a way to calculate the
position restraint energy (for example, if I'm using a posre.itp file
to harmonically restrain some atoms) on the fly. Can anyone give me
some pointers? I haven't turned up anything useful on this since 2001
on the m
Rongliang Wu wrote:
> Hello, gmx-users，
> i want to restrain two molecules, and i have added
>
> #ifdef POSRES
> #include "posre_A.itp"
> #endif
>
> #ifdef POSRES
> #include "posre_B.itp"
> #endif
>
> seperately in coresponding itp files, and add "define = -DPOSRES" to mdp file
>
> but i g
Hello, gmx-users，
i want to restrain two molecules, and i have added
#ifdef POSRES
#include "posre_A.itp"
#endif
#ifdef POSRES
#include "posre_B.itp"
#endif
seperately in coresponding itp files, and add "define = -DPOSRES" to mdp file
but i got error
when i added
#ifdef POSRES_A
#in
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