Hi,
In my simulation, total charge of the system is a noninteger number (System
has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine
atoms.
Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
Fatal error:
moleculetype CU1 is redefined
is it some thing wrong?
Below
On 01/25/11, ahmet yıldırım wrote:
> Hi,
>
> In my simulation, total charge of the system is a noninteger number (System
> has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine
> atoms.
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> Fatal error:
Dear Mark,
I looked at gromacs mail list but I could not find a proper solution
.Whatshould
I add to the .top file? Please look at the following reconstructed1 .top and
reconstructed1 .top files
I have error as the following reconstructed1 .top file:
*Fatal error:*
moleculetype CU1 is redefined
On 01/25/11, ahmet yıldırım wrote:
> Dear Mark,
>
> I looked at gromacs mail list but I could not find a proper solution .What
> should I add to the .top file? Please look at the following reconstructed1
> .top and reconstructed1 .top files
>
>
> I have error as the following reconstructed
Hi
It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get
these problems in explicit solvent simulations on CPU, only in implicit solvent
simulations both on GPU as well as CPU. One of the problems that I can think of
is unbalanced charges that I would have balanced out
Hello,
You have to look into your ions.itp which is included in your top-file by
#include ions.itp.
There all the types of ions have to be defined.
The atom-types which you can see in the ions.itp, you will
find in the ff"your-forcefield".itp where your atomtypes are defined.
On top of your .top f
Dear Mark and Emanuel,
I am sending the ions.tip and the topol.top files. Everything seems ok. Any
problem about these files?
By the way, I am using the Gromacs 4.5.3.
Force Field 43a1
25 Ocak 2011 12:03 tarihinde Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> yazdı:
> Hello,
>
> You h
On 01/25/11, ahmet yıldırım wrote:
> Dear Mark and Emanuel,
>
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any
> problem about these files?
>
No. So one of the other #include files is erroneously defining ion molecule
types. See www.gromacs.org/Documentation/In
Dear Mark,
A million thanks. Problem is solved.
Finally,
Select a continuous group of solvent molecules:
...
Group12 ( Water) has 126219 elements
Group13 (SOL) has 126219 elements
Which one should I choose 12 or 13?
*Final topol.top file:
*;File 'topol.top' was
On 01/25/11, ahmet yıldırım wrote:
> Dear Mark,
>
> A million thanks. Problem is solved.
> Finally,
> Select a continuous group of solvent molecules:
> ...
> Group 12 ( Water) has 126219 elements
> Group 13 ( SOL) has 126219 elements
>
>
> Which one should I choose
Dear users,
g_rms -s em.tpr -f run.xtc
Select group for least squares fit:
Selected 2: 'Protein-H'
Select group for RMSD calculation
Selected 2: 'Protein-H'
I didn't had such a problem in other samples. But now, I have the error as
the following:
Program g_rms, VERSION 4.5.3
Source code file: gm
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
I want to keep the T at 300K, so does it matter to select any thermostat method?
Another note when i use PME:
Hi Ahmet,
That sort of indicates that the file is not there, doesn't it?
Maybe you're not doing what you expect to be doing, or doing it somewhere else.
Cheers,
Tsjerk
2011/1/25 ahmet yıldırım :
> Dear users,
>
> g_rms -s em.tpr -f run.xtc
> Select group for least squares fit:
> Selected 2: 'P
gromacs wrote:
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
I want to keep the T at 300K, so does it matter to select any thermostat
method?
The choi
Dear Tsjerk,
Thank you. Problem solved.
g_rms -s em.tpr -f run.trr -o rmsd.xvg
xmgrace rmsd.xvg
25 Ocak 2011 14:51 tarihinde Tsjerk Wassenaar yazdı:
> Hi Ahmet,
>
> That sort of indicates that the file is not there, doesn't it?
> Maybe you're not doing what you expect to be doing, or doing it s
Hello
I know this is possibly an issue for the IT support at my Uni but I
was wondering if someone could shed some light on what may have gone
wrong so at least I can point them in the right direction.
As I am getting very small diffusion coefficients when using g_msd, I
want to increase
Jennifer Williams wrote:
Hello
I know this is possibly an issue for the IT support at my Uni but I was
wondering if someone could shed some light on what may have gone wrong
so at least I can point them in the right direction.
As I am getting very small diffusion coefficients when using g
Dear gromacs users,
I would like to ask if there is a possibility in gromacs to calculate dipole
moment between two atoms. For example one from water and another one from
ligand.
best,
Olga
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pl
On 2011-01-25 14.51, Olga Ivchenko wrote:
Dear gromacs users,
I would like to ask if there is a possibility in gromacs to calculate
dipole moment between two atoms. For example one from water and another
one from ligand.
best,
Olga
If you mean the combined dipole moment of a particular water
Dear all,
I launched on my system a first simulation of 5 ns, then I prolonged it to
50 ns using
tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I relaunched
it
Anna Marabotti wrote:
Dear all,
I launched on my system a first simulation of 5 ns, then I prolonged it
to 50 ns using
tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, e
Dear David,
I mean a dipole moment between a particle atom in a ligand and a particular
atom in water molecule. G_dipoles works for molecules, as I understood, not
for atoms.
best,
Olga
2011/1/25 David van der Spoel
> On 2011-01-25 14.51, Olga Ivchenko wrote:
>
>> Dear gromacs users,
>>
>> I
On 2011-01-25 16.01, Olga Ivchenko wrote:
Dear David,
I mean a dipole moment between a particle atom in a ligand and a
particular atom in water molecule. G_dipoles works for molecules, as I
understood, not for atoms.
You can measure the distance between them, the dipole moment will be
ill-def
Thank you David,
Olga
2011/1/25 David van der Spoel
> On 2011-01-25 16.01, Olga Ivchenko wrote:
>
>> Dear David,
>>
>> I mean a dipole moment between a particle atom in a ligand and a
>> particular atom in water molecule. G_dipoles works for molecules, as I
>> understood, not for atoms.
>>
>
>
Hi,
I am interested in carrying out umbrella sampling for a protein in explicit
solvent with the charmm forcefield. I want to impose a harmonic potential in
the dihedral space of only some specific atoms in the protein molecule. I am
having trouble figuring out a way to apply this using gromacs. C
Sai Pooja wrote:
Hi,
I am interested in carrying out umbrella sampling for a protein in
explicit solvent with the charmm forcefield. I want to impose a harmonic
potential in the dihedral space of only some specific atoms in the
protein molecule. I am having trouble figuring out a way to ap
Dear Justin,
thank you for your answer. I'm currently using Gromacs version 4.0.7
which was compiled in double precision, therefore I strongly suspect
that this is a problem linked to the old bug. It seems to me that I used
eneconv previously on this machine to concatenate .edr files, but I
cannot
OK, that is what I was trying to figure out -- is the problem
reproducible on both GPU and CPU. Now, you havent answered the direct
question, if the energies are the same for at least the first 5 steps
are so -- without that knowledge, then here might be different errors
occurring in GPU vs CPU.
anna.marabo...@isa.cnr.it wrote:
Dear Justin,
thank you for your answer. I'm currently using Gromacs version 4.0.7
which was compiled in double precision, therefore I strongly suspect
that this is a problem linked to the old bug. It seems to me that I used
eneconv previously on this machine to
Hi all,
I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2.
My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H)
Once I put this on our groups AMD Cluster the jobs fail even wi
Dear users,
How can I fixed the NOTE the following? Will this note/warning cause a
problem in the calculations?What is the meaning of this note?
NOTE 1 [file pr.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
--
Ahmet YILDIRIM
--
gmx-us
Alright. So meaning I should have instead issued:
./configure --enable-mpi --program-suffix=_mpi
make mdrun
make install-mdrun
make links
to have installed an MPI-enabled executable called mdrun_mpi apart from the
existing mdrun executable? (Would I also need to append the _mpi suffix when
is
On 26/01/2011 8:10 AM, ahmet yıldırım wrote:
Dear users,
How can I fixed the NOTE the following? Will this note/warning cause a
problem in the calculations?What is the meaning of this note?
NOTE 1 [file pr.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm
On 26/01/2011 8:50 AM, Justin Kat wrote:
Alright. So meaning I should have instead issued:
./configure --enable-mpi --program-suffix=_mpi||
make mdrun
make install-mdrun
make links
to have installed an MPI-enabled executable called mdrun_mpi apart
from the existing mdrun executable? (Would I a
On 26/01/2011 12:05 AM, Justin A. Lemkul wrote:
gromacs wrote:
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale
thermostat.
I want to keep the T at 300K, so does it ma
On 26/01/2011 5:50 AM, TJ Mustard wrote:
Hi all,
I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and
FFTW 3.2.2.
My iMac will run the job (over 4000 steps, till I killed it) at 4fs
steps. (I am using heavy H)
Once I put this on our groups AMD Cluster the jobs fail even w
On January 25, 2011 at 2:08 PM Mark Abraham wrote:
On 26/01/2011 5:50 AM, TJ Mustard wrote:
Hi all,
I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2.
TJ Mustard wrote:
On January 25, 2011 at 2:08 PM Mark Abraham wrote:
On 26/01/2011 5:50 AM, TJ Mustard wrote:
Hi all,
I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and
FFTW 3.2.2.
My iMac will run the job (over 4000 steps, till I killed it) at 4fs
step
Dear Justin/Mark,
I would like to have a private course about Gromacs in Holland.
Is there such a facility for this? Who should I talk with?
Or is there a workshop in near future?
best wishes
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pl
On January 25, 2011 at 3:24 PM "Justin A. Lemkul" wrote:
>
>
> TJ Mustard wrote:
> >
> >
> >
> >
> >
> > On January 25, 2011 at 2:08 PM Mark Abraham wrote:
> >
> >> On 26/01/2011 5:50 AM, TJ Must
Hi,
There are two things you should test:
a) Does your NVIDIA driver + CUDA setup work? Try to run a different
CUDA-based program, e.g. you can get the CUDA SDK and compile one of
the simple programs like deviceQuery or bandwidthTest.
b) If the above works, try to compile OpenMM from source with
On 01/26/11, TJ Mustard wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On January 25, 2011 at 3:24 PM "Justin A. Lemkul"
> wrote:
>
>
>
> >
>
> >
>
> > TJ Mustard wrote:
>
> > >
>
> > >
>
> > >
>
>
TJ Mustard wrote:
> 1. Do the systems in question crash immediately (i.e., step zero) or
do they run
> for some time?
>
Step 0, every time.
> 2. If they give you even a little bit of output, you can analyze
which energy
> terms, etc go haywire with the tips listed here:
>
All
trevor brown wrote:
Dear Justin/Mark,
I would like to have a private course about Gromacs in Holland.
Is there such a facility for this? Who should I talk with?
Can't help you there. I'm in the U.S.
Or is there a workshop in near future?
Any workshops will surely be announced on the
On January 25, 2011 at 3:54 PM Mark Abraham wrote:
On 01/26/11, TJ Mustard wrote:
On January 25, 2011 at 3:53 PM "Justin A. Lemkul" wrote:
>
>
> TJ Mustard wrote:
>
>
>
> > > 1. Do the systems in question crash immediately (i.e., step zero) or
> > do they run
> > > for some time?
>
Hi Justin,
.mdp and fourierspacing are at below, can you tell me where is not wrong?
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (v
gromacs wrote:
Hi Justin,
.mdp and fourierspacing are at below, can you tell me where is not wrong?
I see nothing "wrong" with the .mdp file, per se, although it does not appear
complete (no integrator, nsteps, etc). Perhaps that was your intention, but if
nsteps is left at defau
Hi,
I am trying to find the free energy of a water molecule as it adsorbs
on a surface. My outline is:
1) Run the simulation
2) Analyze the results, find out which water molecule(s) are adsorbed
3) Create different groups for the water adsordbed molecule(s), create
new .gro file (to identify
On 01/26/11, Shalabh wrote:
> Hi,
>
> I am trying to find the free energy of a water molecule as it adsorbs on a
> surface. My outline is:
>
> 1) Run the simulation
> 2) Analyze the results, find out which water molecule(s) are adsorbed
> 3) Create different groups for the water adsordbed mo
Hi, All,
I'm trying to see if anybody has experience of using the interface of
gromacs and ORCA(since it's free). I know that the following link gave
information on how
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
But.But, the gromacs in the above link is quite old(3.2). I
download
Hi,
I ran a simulation of 10ns and now it has completed till 5ns .. I want to
stop it now and retrieve the trajectories without any errors.. Is it
possible to do that ??
--
Bharat
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