Thanks Prof. David.
I've done all that now, but at the moment I'm locked getting lots of the
"lovelly" error:
Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your syste
Jones de Andrade wrote:
Hi all.
Well, I'm having a bit of trouble here because the work has decided to
go in the direction of something I've never used before with gromacs:
dummy atoms (or now "virtual sites").
I assume this is not for a protein, in which case pdb2gmx does it for you.
I've
Bruce Milne wrote:
You don't have to run pdb2gmx for the whole system at any point
Probably true.
(it's
not going to work anyway unless you add the POPC parameters to all the
force field files and then add the POPC residue to the .rtp file so
that pdb2gmx can recognize it).
Not quite tr
Hi all.
Well, I'm having a bit of trouble here because the work has decided to go in
the direction of something I've never used before with gromacs: dummy atoms
(or now "virtual sites").
I've got at least three questions in order to use them:
1 - does the virtual sites need to be included in the
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_
residue_topology_database
You only run pdb2gmx on molecules that you want to generate a topology
file for. For the lipids, you will already have the .itp files for it,
or should have. So you don't run pdb2gmx on it.
Catch
Well, yeah. But I want to look at the HOMO-LUMO gap of the system in the living
environment. Since the system is too big to do MD with the QM code, I tried to
use the best force field description I could, and the smallest box as well, to
get structures that could represent the system at 300K. And
Dear Adak,
[EMAIL PROTECTED] wrote:
Dear All;
when I try to run pdb2gmx command for making .top file of POPC+Protein, an
error appears: Residue 'POPC' not found in residue topology database.
I have copied all necessary .itp files in share folder and also in the path
where it is run.
what cou
HI David,
I used -DPOSRE, no constraints but temperature coupling (berendsen), no
pressure coupling.
thanks,
Luciano
> luciano.pgomes wrote:
> > Hi,
> >
> >> Hi All,
> >>
> >> I had this problem running MD on a single Debian machine:
> >>
> >> Program mdrun_d, VERSION 3.3.1
> >> Source code fil
Ah, okay thanks very much! I thought-sure I had the most recent version,
but apparently not. Still there's one quirk...
x2top -f HexA.gro -o HexA.top -r HexA.rtp -alldih
...This works to generate a topology file, but still, the program is
seg-faulting before writing out the residue type file (*.
Much appreciated, works beautifully!
On 10/10/07, TJ Piggot <[EMAIL PROTECTED]> wrote:
>
> Just as a note editconf will covert a pdb to a gro file
>
> Tom
>
> --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser
> <[EMAIL PROTECTED]> wrote:
>
> > Yes I tried this and it doesn't work for me.
Dear All;
when I try to run pdb2gmx command for making .top file of POPC+Protein, an
error appears: Residue 'POPC' not found in residue topology database.
I have copied all necessary .itp files in share folder and also in the path
where it is run.
what could be the problem and how to solve it?
luciano.pgomes wrote:
Hi,
Hi All,
I had this problem running MD on a single Debian machine:
Program mdrun_d, VERSION 3.3.1
Source code file: stat.c, line: 257
Fatal error:
XTC error
There is no chance of being size exceeded of file or quota, or disk error.
I compiled gromacs with gcc-3.4..
[EMAIL PROTECTED] wrote:
Thank you very much again, David! Then it's fine for me, since what I want to
do is a single point QM in "termalized" snapshots of the dynamics and not QM
minimization.
But then you will get systematically incorrect energies due to weird
(force field dependent) bond len
Hi,
> Hi All,
>
> I had this problem running MD on a single Debian machine:
>
> Program mdrun_d, VERSION 3.3.1
> Source code file: stat.c, line: 257
>
> Fatal error:
> XTC error
>
>
> There is no chance of being size exceeded of file or quota, or disk error.
> I compiled gromacs with gcc-3.4...
>
Thanks for your suggestions,
I have gone for the solution where I change the type of group numbers
from uchars to unsigned short.
It seems however that this solution is not very elegant:
I fail to understand the logic of limiting the number of groups in the
energygrp_table field to 254. Indeed t
Just as a note editconf will covert a pdb to a gro file
Tom
--On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser
<[EMAIL PROTECTED]> wrote:
Yes I tried this and it doesn't work for me. I get:
Fatal error:
Library file ffG53a6.n2t not found in current dir nor in default
directories.
Thank you very much again, David! Then it's fine for me, since what I want to
do is a single point QM in "termalized" snapshots of the dynamics and not QM
minimization.
Gustavo
> [EMAIL PROTECTED] wrote:
> > Dear GROMACS Users,
> >
> > I'm trying to use GROMACS to get some MD snapshots for s
Adam Fraser wrote:
Yes I tried this and it doesn't work for me. I get:
Fatal error:
Library file ffG53a6.n2t not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
did you use 3.3.2 ? The default and only supported FF ther
Yes I tried this and it doesn't work for me. I get:
Fatal error:
Library file ffG53a6.n2t not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script that
convert
Adam Fraser wrote:
Hello,
I'm very new to Gromacs, and I am interested in simulating the
interactions of 2 hexadecane (C16H34) molecules in water (SPC/E
specificall). I've spent some time experimenting with tutorials in
Gromacs, but I've found little help in non-protein simulations like this
Hello,
I'm very new to Gromacs, and I am interested in simulating the interactions
of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent
some time experimenting with tutorials in Gromacs, but I've found little
help in non-protein simulations like this one.
I've built topolo
[EMAIL PROTECTED] wrote:
Dear GROMACS Users,
I'm trying to use GROMACS to get some MD snapshots for single-point quantum
mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed
in water with counterions, at a given salt concentration (4600 atoms in total).
I'd like to kn
luciano.pgomes wrote:
Hi All,
I had this problem running MD on a single Debian machine:
Program mdrun_d, VERSION 3.3.1
Source code file: stat.c, line: 257
Fatal error:
XTC error
it can also mean that your system is exploding.
There is no chance of being size exceeded of file or quota, or
Hi All,
I had this problem running MD on a single Debian machine:
Program mdrun_d, VERSION 3.3.1
Source code file: stat.c, line: 257
Fatal error:
XTC error
There is no chance of being size exceeded of file or quota, or disk error.
I compiled gromacs with gcc-3.4...
Does anyone know what this
Hi,
When running grompp I get the following error often
###
checking input for internal consistency...
WARNING 1 [file md-new.mdp, line unknown]:
###
It does not look like a critical error, but I want to make sure. Did not
find any specific discussions on the mailing list immediately.
My
From: "WU Yanbin" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] How to change the box size during simuation
Date: Tue, 9 Oct 2007 17:40:21 -0500
Hey,
Now I'm simulating infinite molecules. I want to change the box size a
lit
Have you simulated the system without the annealing, to see if it does the same
thing? Bilayers are very sensitive to minor changes in setup, using someone
else's equilibrated bilayer coordinates doesn't mean it's equilibrated for your
system.
- Original Message
From: Q733 <[EMAIL PR
You can apply external forces to subsets of atoms, in such a way as to cause
your box to shrink by itself.
- Original Message
From: WU Yanbin <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, October 9, 2007 11:40:21 PM
Subject: [gmx-users] How to change the box size during s
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