http://manual.gromacs.org/documentation/current/onlinehelp/gmx-covar.html
Has the following note (as does 'gmx help covar'):
"Note that the diagonalization of a matrix requires memory and time
that will increase at least as fast as than the square of the number
of atoms involved. It is easy to run
Dear GROMACS Developers and users,
While trying to clustering analysis based on certain distance matrices,
however, while trying to perform PCA, I executed the following command, it
shows the following error. Need your valuable suggestion and feedback to get
rid of such errors.
Thanking you
I got the following error while running the gromacs
*NOTE: disabling dynamic load balancing as it is only supported with
dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP
threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected
for
Thanks, for your help.
Em seg, 11 de mar de 2019 às 19:31, Justin Lemkul
escreveu:
>
>
> On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote:
> > If i don't use -maxwarn option they send me the same error.
>
> Omitting -maxwarn won't fix problems, but it is a very bad habit to
> casually
On 3/11/19 5:45 PM, Mario Andres Rodriguez Pineda wrote:
If i don't use -maxwarn option they send me the same error.
Omitting -maxwarn won't fix problems, but it is a very bad habit to
casually use -maxwarn as it overrides critical problems with your input.
I see also this:
WARNING 1
If i don't use -maxwarn option they send me the same error.
I see also this:
WARNING 1 [file topol.top, line 23986]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform
On 3/11/19 3:20 PM, Mario Andres Rodriguez Pineda wrote:
Hi everybody
I want to do one dynamic simulation of one protein
i'm try to minimize the protein in vacum before the simulation runing but
gromacs send me this error:
---
Program:
Hi everybody
I want to do one dynamic simulation of one protein
i'm try to minimize the protein in vacum before the simulation runing but
gromacs send me this error:
---
Program: gmx grompp, version 2018.6
Source file:
You really need cuda? IF no you can try:cmake .. -DGMX_GPU=OFF
On Sunday, October 29, 2017, 7:26:04 AM GMT+2, Kunal Dutta
wrote:
Hi,
I have the following problems
kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
Hi,
I have the following problems
kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON
CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message):
The GROMACS build will download FFTW 3.3.3 as requested, but it will not
know the file it
On 10/16/17 12:17 PM, Rahma Dahmani wrote:
Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.
Either correct the atom names to what the force field expects, or
simplify life and use
Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.
Thank you for your help
--
*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé,
Hi,
It's hard to say, but you should look at the log file and terminal output,
and install the latest in the series of bug fixes... 5.0.7 rather than
choose a version known to have dozens more bugs...
Mark
On Tue, Sep 12, 2017 at 3:55 PM Vidya R wrote:
> Hi,
>
> I
Hi,
I fixed that error.
However,I now encounter a new one...
GROMACS:gmx grompp, VERSION 5.0.2
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit Groenhof
Hi,
Yeah I've never seen that, so I assume it's something weird related to how
GROMACS was originally compiled vs how the system has been updated since.
Since a rebuild is the way to investigate that, definitely update to at
least the latest 5.0.x while you do it.
Mark
On Mon, Sep 11, 2017 at
On Mon, Sep 11, 2017 at 8:44 AM, Vidya R wrote:
> Hi,
>
>
> When I give these two commands
>
> gmx grompp -f mdp/min.mdp -o min -pp min -po min
> gmx mdrun -deffnm min
>
> I get this error.
>
> What to do?
>
>
>
> Reading file min.tpr, VERSION 5.0.2 (single precision)
>
Hi,
When I give these two commands
gmx grompp -f mdp/min.mdp -o min -pp min -po min
gmx mdrun -deffnm min
I get this error.
What to do?
Reading file min.tpr, VERSION 5.0.2 (single precision)
tMPI error: tMPI Initialization error (in valid comm)
Thanks,
Vidya.R
--
Gromacs Users mailing
Dear All,
I have produced the "ITP" files of the ligands using ATB server. I am
mentioning the steps here, please let me know if you think anything is
wrong.
a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.
b) Entered the "net charge" by
On 8/29/17 12:09 AM, Neha Gupta wrote:
Hi Vytautas,
Thank you for your response..
I did as you told and got this message at the command prompt
libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a
But the error tells me :
gmx: error while loading shared libraries:
Hi Vytautas,
Thank you for your response..
I did as you told and got this message at the command prompt
libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a
But the error tells me :
gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such
Make sure you have libfftw3f installed properly. In such case command:whereis
libfftw3fshould give you location of that file which gmx is unable to find.
On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta
wrote:
Hi gromacs users,
How to fix this error?
gmx:
Hi gromacs users,
How to fix this error?
gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory
PATH=$PATH:"/usr/local/gromacs/bin/"
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"
Thanks,
Neha
--
Gromacs
On 2/1/16 1:06 AM, Mehreen Jan wrote:
how to run gromacs for protein protein interaction having phosphorylated at SER
and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields
how to run gromacs for protein protein interaction having phosphorylated at SER
and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields
>make changes in .rtp file
make changes in
Hello
I am doing Protein-Ligand simulation and I face following error while
running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o
em.tpr". Kindly assist me how can I rectify error ?
Error
Program grompp, version 3.3.3
source code file: toppush.c, line: 1396
2015 7:33 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gromacs error
Hello
I am doing Protein-Ligand simulation and I face following error while
running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o
em.tpr". Kindly assist me how can I rectify error
Hi Manoj,
The error is clear. Check the settings referred to in your .mdp file and
modify them accordingly.
Cheers,
Tsjerk
On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in
wrote:
Dear All,
i'm geting below error while subjecting my system (Protein-ligand) for
equlibriation
ERROR 1 [file nvt.mdp]:
With coulombtype = PME-Switch, rcoulomb must be = rlist
On Tue, May 19, 2015 at 10:25 AM, manoj damale
manojaurangabad...@yahoo.co.in wrote:
what exactly i should modify
With Best Regards.
Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West
Dear All,
i'm geting below error while subjecting my system (Protein-ligand) for
equlibriation in nvt.mdp file
mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p
topol.top -n index.ndx -o nvt.tpr
:-) G R O M A C S (-:
Dear Gromacs users
we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial).
This pdf file contains two cofactors including TPF and HEM. Our next step is to
dock some antifungal drugs to this protein which is cytochrome of the fungi.
As the TPF was not located in the
hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
Command 'gcx' from package 'gcx' (universe)
On 9/22/14 10:14 AM, Yaser Hosseini wrote:
hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
How should I correct the input file?
Urszula Uciechowska
On 7/31/14, 7:42 AM, Urszula Uciechowska wrote:
Dear Gromacs users,
I tried to run coarse grained MD however after a few steps I got:
Step 39, time 0.78 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038933,
On 7/31/14, 8:16 AM, Urszula Uciechowska wrote:
How should I correct the input file?
http://manual.gromacs.org/online/mdp_opt.html#vel
And get your hands on some suitable tutorial material; proper use of these
settings is routine.
-Justin
Urszula Uciechowska
On 7/31/14, 7:42 AM,
Can anyone help me with this error file? I did not get the log file...
Back Off! I just backed up md.log to ./#md.log.5#
Reading file md10ns-2.tpr, VERSION 4.5.3 (single precision)
Reading checkpoint file md10ns.cpt generated: Mon Jul 21 20:45:14 2014
Gromacs binary or parallel settings not
On 7/31/14, 8:36 AM, Urszula Uciechowska wrote:
Can anyone help me with this error file? I did not get the log file...
There is no error here. I assume this is what is concerning:
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not
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