On May 16, 2014 11:36 PM, "Koki Yokoi" wrote:
>
> Hello. I am currently using GROMACS4.6.5 and trying to simulate a
fluorescent protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine
receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme
part(res#1002-1161), so I removed it to make
Your simulation seems too small to parallelize in the way you/mdrun tried.
But we need more information to be sure.
Mark
On May 17, 2014 7:33 AM, "Lovika Moudgil" wrote:
> Hi Everyone
> I need some help. With my mdrun command I am getting this following error
> .
>
> Program mdrun, VERSION
Hi Everyone
I need some help. With my mdrun command I am getting this following error .
Program mdrun, VERSION 4.6.5
Source code file:
/home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line:
722
Fatal error:
DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connect
What Michael said, and if your .mdp setup triggers a code path for which
the implementation changed between 4.0.7 and 4.5.5 (like it did for at
least twin-range), then you should see different behaviour. But I guess
we'll have to keep making unproductive guesses.
Mark
On Fri, May 16, 2014 at 11:
Berendsen has the right average volume, but not the right distribution of
volumes.
http://pubs.acs.org/doi/abs/10.1021/ct300688p
Did you equilibrate berendsen until the volume stabilized and THEN switch
to parrinello-rahman for production? That's the suggested thing to do.
On Fri, May 16, 2014
Hello. I am currently using GROMACS4.6.5 and trying to simulate a fluorescent
protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine
receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme
part(res#1002-1161), so I removed it to make the simulation consistent with our
experimenta
One initial structure is equilibrated for 10ns using Gromacs VERSION
4.0.7. If I run same structure with same .mdp and same force field
parameters using gromacs VERSION 4.5.5. I got the error system is
blowing up.
I made another new initial structure which is not equilibrated and I got
the same
Unstable models or unstable initial conditions will behave unpredictably.
Unfortunately you've not given us much to go on.
Mark
On May 16, 2014 6:08 PM, "Nilesh Dhumal" wrote:
> >
> >
> > On 5/16/14, 11:37 AM, Nilesh Dhumal wrote:
> >> Hello,
> >>
> >> I am running the simulation for ionic liqui
On May 16, 2014 7:03 PM, "Juan Munoz-Garcia" <
juan.munoz-gar...@bioch.ox.ac.uk> wrote:
>
> Dear Justin,
>
> thank you. I’ve tried the following but neither of them worked, I get the
same result.
>
> trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol
-ur compact
>
> trjconv -f
Dear Justin,
thank you. I’ve tried the following but neither of them worked, I get the same
result.
trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur
compact
trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc
mol -ur compact
This is the
>
>
> On 5/16/14, 11:37 AM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I am running the simulation for ionic liquids. I initially did
>> simulation
>> with Gromacs VERSION 4.0.7 with "parrinello-rahman" pressure coupling.
>> Here I pasted temperature and pressure coupling part of mdp file.
>>
>> ; Tempe
Hi Abraham,
When I do the indexing, the hbndx gives all h-bonds in ascending order for
all frames and i see the a lot of repeated bonding with the same acceptor
atom. Is it possible to get the index for a particular frame? I see the
option -dt but i didn't quite get that one. Also, the hbnum.xvg fi
On 5/16/14, 11:37 AM, Nilesh Dhumal wrote:
Hello,
I am running the simulation for ionic liquids. I initially did simulation
with Gromacs VERSION 4.0.7 with "parrinello-rahman" pressure coupling.
Here I pasted temperature and pressure coupling part of mdp file.
; Temperature coupling is on
Tc
Hello,
I am running the simulation for ionic liquids. I initially did simulation
with Gromacs VERSION 4.0.7 with "parrinello-rahman" pressure coupling.
Here I pasted temperature and pressure coupling part of mdp file.
; Temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps =system
r
On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote:
Thank you Justin,
please find a dropbox link to the image below.
I’ve used
trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center
and different combinations of th
Thank you Justin,
please find a dropbox link to the image below.
I’ve used
trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center
and different combinations of those
https://www.dropbox.com/s/az1gvb299y6wh8h/Scr
On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote:
Dear GROMACS users,
I’m preparing a protein-membrane structure to use as input for MD. I’ve just
carried out a short minimisation of the lipids applying restraints to the
protein, after which I’ve obtained the attached structure. I’ve tried all
typ
Dear GROMACS users,
I’m preparing a protein-membrane structure to use as input for MD. I’ve just
carried out a short minimisation of the lipids applying restraints to the
protein, after which I’ve obtained the attached structure. I’ve tried all types
of trjconv combinations with -pbc -ur or -fi
Dear GROMACS users,
I’m preparing a protein-membrane structure to use as input for MD. I’ve just
carried out a short minimisation of the lipids applying restraints to the
protein, after which I’ve obtained the attached structure. I’ve tried all types
of trjconv combinations with -pbc -ur or -fi
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