Hi ALL,
I have a protein pdb file generated using MODELLER. When I use the pdb2gmx
command on it, it throws the error:
Atom -C not found in residue MET1 while adding hydrogens
and
Atom OXT in residue LEU 404
The initial and end of the pdb file is like this:
-
Hi,
I did some experiments with a harmonic oscillator (diatomic molecule
without charge en LJ parameters) using the v-rescale thermostat. First I
ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total
energy was constant here.
Then I tried simulating the system with the v-resca
Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all. afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check file
Hi,
What do you mean with effective energy?
The Gromacs conserved energy term?
For very small tau_t the current implementation does not work well.
Bussi mailed me a proper implementation that I will put in when I have time.
Berk
> From: servaas.michielss...@student.kuleuven.be
> To: gmx-users@
Dear all,
I'm running a simulation of a structure which has part of ATP bound to
it so I'm using the -missing command when running pdb2gmx
pdb2gmx runs and lists the missing atoms and than it gives a fatal error
about missing atom name!
WARNING: atom O3PB is missing in residue ATP 340 in th
Anirban Ghosh wrote:
Hi ALL,
I have a protein pdb file generated using MODELLER. When I use the
pdb2gmx command on it, it throws the error:
What is your pdb2gmx command line? It looks like a -ter issue.
Atom -C not found in residue MET1 while adding hydrogens
and
Atom OXT in residue LE
Hi,
Thank you for your reply.
Yes by effective energy I mean the Gromacs conserved energy term.
So you would say the cause of my problem here is that I need a small
tau_t to thermostat this system but for small tau_t values the algorithm
is not 100% ok yet? And what are very small tau_t values?
Zhanglin Ni wrote:
Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all. afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in ti
Una Bjarnadottir wrote:
Dear all,
I'm running a simulation of a structure which has part of ATP bound to
it so I'm using the -missing command when running pdb2gmx
pdb2gmx runs and lists the missing atoms and than it gives a fatal error
about missing atom name!
WARNING: atom O3PB is missi
Thank you for answer.
I checked up my .gro and .top files, and even I make it from pdb using pdb2gmx,
simulation crashes. But without constraints or with all-bonds constraint, it
work
finely. But all-angles constraint results warnings (no p-coupling):
--
Step 0, time 0 (ps) LINCS WARNING
relative
Please help !
I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end of
the simulation, I have a bilayer, but it is not at the center of the box.
Instead, it has two leaflets on each edge of the box separated by water,
with the bilayer normal along the x-axis. How can I realign th
maria goranovic wrote:
Please help !
I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end
of the simulation, I have a bilayer, but it is not at the center of the
box. Instead, it has two leaflets on each edge of the box separated by
water, with the bilayer normal along th
Hi,
No, only for small values is should be off, maybe tau_t < 10 or 100 * delta_t.
How did you set up your harmonic oscillator?
Berk
> From: servaas.michielss...@student.kuleuven.be
> To: gmx-users@gromacs.org
> Date: Thu, 7 May 2009 12:54:54 +0200
> Subject: [gmx-users] Re: v-rescale - harmo
I agree with Justin that the way to do this is by adding a new entry to the
.rtp file. The only point I would make is that as you seem to be missing
the gamma phosphate and its oxygens would it not make more sense to start
from an ADP topology? Also you should ask (or have asked) yourself why
t
t; > http://www.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 po
gt; > > >
> > > > Thanks in advance,
> > > >
> > > > Servaas
> > > >
> > >
> > > ___
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://www.groma
zawieszla sie jeszcze szmaciarz?
gmx-users-requ...@gromacs.org wrote:
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Hi Berk,
Thank you for your concern on this issue. It did not expect it to be a
problem from the paper of Bussi et al., but it is of course possible.
I am very curious to hear what they have to say about this. Are you
contacting him or will I do it?
For the rotational degrees of freedom would re
At 12:35 PM 5/7/2009, you wrote:
Please help !
I ran a simulation of self-assembly of a DPPC lipid bilayer. At the
end of the simulation, I have a bilayer, but it is not at the center
of the box. Instead, it has two leaflets on each edge of the box
separated by water, with the bilayer normal
Thank you Justin. The following option worked for me:
-center -boxcenter zero -pbc mol
with the centering done around the lipid.
Sincerly
-Maria
Message: 3
> Date: Thu, 07 May 2009 07:41:50 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Recentering box after simulation of
>
Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Any clues from any of the other *.out files?
-Justin
Zhanglin Ni wrote:
Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in t
Dear all:
I finished a MD simulation and i want to calculation the
correlation fluctuation of the alpha C.Does there any tools that can
do this in gromacs package (I have tried g_rmsf -oc , but it doesn't
work,specificly, the -oc command give no result) ?
Can any one be so k
Dear All:
I am working on a large polymer molecule system. The single molecules has a
dimension of 5nm. My question is how can I set up the cut-off in my md.mdp.
I tried the cut-off of 1.2 and got the following two notes:
NOTE 1 [file md.mdp, line unknown]:
The Berendsen thermostat does not g
Thank you for answer.
I checked up my .gro and .top files, and even if I make it from pdb using
pdb2gmx,
simulation crashes. But without constraints or with all-bonds constraint, it
work
finely. But all-angles constraint results warnings (no p-coupling):
--
Step 0, time 0 (ps) LINCS WARNING
rela
Dear users:
I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no
error message. However I found that in the gro file by visualization, 2 of
the chains has been split in many parts, which means many bonds in the
molecules disconnected. And also the other 4 are good. I checked
Yanmei Song wrote:
Dear users:
I set up a 8nm cubic box with 6 long chain molecules. After EM, there is
no error message. However I found that in the gro file by visualization,
2 of the chains has been split in many parts, which means many bonds in
the molecules disconnected. And also the o
Hi Yanmei,
I had this problem with water molecules, and I found that any time I changed
the constrains without changing the boxes I generated through 'editconf'.
So, after changing the constrains, I had to redo all my box generation
process, then it was fine. But I ran into another problem and tha
The checkvir.out files looked like (I just show last few lines here):
Pressure (bar) step 50: 46893.3, step 50:44603
Vir-XY step 50: -2423.21, step 50: -1880.2
Vir-XZ step 50: 667.327, step 50: 307.438
Vir-YX step 50:
Hi, Berk
Thank you for your reply, finally I solved this by modifying the mdp
options.
'Cause I want to use PME in 2-dimensional periodic system to compute
electrostatic, I have to
set up the virtual walls with mdp option nwalls=2 in Gromacs. It succeeded
to set up the simualtion system.
Origina
Zhanglin Ni wrote:
The checkvir.out files looked like (I just show last few lines here):
Pressure (bar) step 50: 46893.3, step 50:44603
Vir-XY step 50: -2423.21, step 50: -1880.2
Vir-XZ step 50: 667.327, step 50: 307.438
Vir-YX
Hi All,
I have just executed my first mdrun and it appears that the default bond
parameters from x2top were used instead of the bond parameters from the
oplsaa force field files which are included in my .top file.
Here is an extract from my .top file with the include statement:
**
darre...@ece.ubc.ca wrote:
Hi All,
I have just executed my first mdrun and it appears that the default bond
parameters from x2top were used instead of the bond parameters from the
oplsaa force field files which are included in my .top file.
Right; if you have explicit definitions of bonds in
Sorry, but I only performed a couple of runs using the test-set, so
don't have a lot of experience, but when I did and got some fails all
the information was there to help point out what the issue was.
Doesn't the files in the subdirectories for each of the tests provide
details of why that partic
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Dear Sirs:
I wang to know simulate coarse-graied system using gromacs, but I don not
know how to use atom2cg.awk to convert CG model!
Thank you very much!
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