Dear all,
I am simulating a system consisting urea molecules. After successfully
generating tpr file while I am trying to run mdrun, the following error is
appearing.
Fatal error:
There is no domain decomposition for 72 ranks that is compatible with the
given box and a minimum cell size of 0.59
This is an issue with CGenFF, nothing to do with GROMACS.
So you need to ask this question through the CGenFF help channel(s),
wherever that may be.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade
Hi All,
I have created a crystal structure of 2 polymer chains (PEG) and I need to
calculate the cohesive energy for my system using CHARMM36 FF. In this case my
fix_mol2 file includes 2 ligands, to convert to str file I get the following
error:
readmol2 warning: non-unique atoms were renamed.
Hi All,
I have created a crystal structure of 2 polymer chains (PEG) and I need to
calculate the cohesive energy for my system using CHARMM36 FF. In this case my
fix_mol2 file includes 2 ligands, to convert to str file I get the following
error:
readmol2 warning: non-unique atoms were renamed.
On 8/20/19 5:56 PM, Anh Vo wrote:
Hi everyone,
I have submitted pbs files to run GROMACS on a high performance computing
cluster, but I received error files showing these messages:
"...
librdmacm: Warning: couldn\'t read ABI version.
librdmacm: Warning: assuming: 4
librdmacm: Fata
On 8/20/19 1:36 PM, Alex Mathew wrote:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
The protocol in the tutorial is simply the elimination of LJ parameters
to compute the vdW contribution to free energy of solvation. It is not
(by desig
Hi everyone,
I have submitted pbs files to run GROMACS on a high performance computing
cluster, but I received error files showing these messages:
"...
librdmacm: Warning: couldn\'t read ABI version.
librdmacm: Warning: assuming: 4
librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
>
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On Tue, Aug 20, 2019 at 9:44 AM Akshay wrote:
> Hello All,
>
> I seem to be having a very particular issue with the Charmm36M force-field
> available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue
> occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal
> when t
Dear Users,
I am getting reasonable performance from two rtx -2080ti's - AMD 32 core and on
another node two gtx-1080 ti's -AMD 16 core i.e 20-30 ns/day with 30 atoms.
But in all my runs the % usage of the gpu's is typcially 40% to 60 % . Given
that it is specialized software, I notice tha
If your trajectory has position information, then yes, it can be used to
compute potential energies.
> Thank you for your reply sir. In this case can I use .The file to compute
> potential energies.
>
> On Tue 20 Aug, 2019, 4:40 PM Mark Abraham,
> wrote:
>
>> Hi,
>>
>> You're doing a rerun from a
Hi,
You can use only GROMACS versions that gromos++ supports. Hopefully they've
documented which ones those are :-)
Mark
On Tue, 20 Aug 2019 at 15:47, Johannes Hermann
wrote:
> Hi Justin,
>
> Thanks! So this is a gromos++ problem? The gromos++ developers should
> update the linking during inst
Hi Justin,
Thanks! So this is a gromos++ problem? The gromos++ developers should
update the linking during installation, right?
All the best
Johannes
On 20.08.19 15:11, Justin Lemkul wrote:
On 8/20/19 8:56 AM, Johannes Hermann wrote:
Dear all,
I am currently installing gromos++ analysis
Hello All,
I seem to be having a very particular issue with the Charmm36M force-field
available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue
occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal
when the C-terminal residue is a Proline.
Then, when subsequent
Thank you for your reply sir. In this case can I use .The file to compute
potential energies.
On Tue 20 Aug, 2019, 4:40 PM Mark Abraham, wrote:
> Hi,
>
> You're doing a rerun from a trajectory file that probably doesn't have
> velocities in it. mdrun can compute potential energies from the posit
Dear Szilard,
thanks for the very clear answer.
Following your suggestion I tried to run without DD; for the same system I
run two simulations on two gpus:
gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
-gputasks 00 -pin on -pinoffset 0 -pinstride 1
gmx mdrun -deffnm run2 -nb
On Mon, Aug 19, 2019 at 12:00 PM tarzan p wrote:
>
> Hi all.I have a dual socket Xeon GOLD 6148 which has the capabilities for
>
> Instruction Set Extensions Intel® SSE4.2, Intel® AVX, Intel® AVX2, Intel®
> AVX-512
> but hen why si gromacs giving the error for AVX_512 but takes AVX2_256???
> A
On 8/20/19 8:56 AM, Johannes Hermann wrote:
Dear all,
I am currently installing gromos++ analysis software. When I link my
Gromacs 2018.6 or 2016.6 installation, I get the error:
../../contrib/gromacs2gromos.cc:101:30: fatal error:
gromacs/typedefs.h: No such file or directory
However,
Thank you very much sir. I will check
On 8/18/19, Justin Lemkul wrote:
>
>
> On 8/18/19 2:06 PM, Dr Adekunle Rowaiye wrote:
>> Hello all,
>> I need help. I got this while doing simulation. What do I do?
>>
>> File input/output error:
>> protein_pr.gro
> This means that either (1) if this is an inp
Dear all,
I am currently installing gromos++ analysis software. When I link my
Gromacs 2018.6 or 2016.6 installation, I get the error:
../../contrib/gromacs2gromos.cc:101:30: fatal error: gromacs/typedefs.h:
No such file or directory
However, if I link my gromacs 5.1.4 installation everythi
On 8/20/19 7:51 AM, Omkar Singh wrote:
Hello gromacs users,
I am working on protein-water system. I am trying to calculate
top(tetrahedral order parameter) by "gmx hydorder" command. After finding
xpm how to proceed for xvg format.
gmx hydorder does not produce such output. You may want to
On 8/20/19 5:21 AM, Jorden Cabal wrote:
Hi Justin,
Thank you for your response. In my case the cost of increasing simulation
box is very large. I have already tried it by keeping distance between the
periodic images of the macromolecule up to 50 Angstrom. Could you suggest
me any other option
On 8/20/19 2:11 AM, Lei Qian wrote:
Thank you Dr. Lemkul,
Could I ask one more question? Thank you!
When I did the step for adding ions and minimization and equilibration
steps, one warning always showed up.
So I had to add -maxwarn 2 after the command gmx grompp.
This warning is as follows:
Hi Carlos,
> Am 20.08.2019 um 13:12 schrieb Carlos Navarro :
>
> Dear gmx-users,
> I'm currently investigating ion permeability in a channel that displays
> multiple cavities through ComEl simulations. Unfortunately one can just
> define a single cylinder per membrane.
Yes, this counting of ion p
Hello gromacs users,
I am working on protein-water system. I am trying to calculate
top(tetrahedral order parameter) by "gmx hydorder" command. After finding
xpm how to proceed for xvg format.
Thanks
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you can go to ccl.net
I am also looking for the postdoctoral position in biological molecule
simulations
Warm Regards
Akhil Kumar
Research Associate
IISc Bangalore
INDIA.
#09839263326
On Tue, Aug 20, 2019 at 11:55 AM Peter Mawanga <
peter.mawanga.la...@gmail.com> wrote:
> Hello everyone
>
> Can
Dear gmx-users,
I'm currently investigating ion permeability in a channel that displays
multiple cavities through ComEl simulations. Unfortunately one can just
define a single cylinder per membrane. Considering the size of my system
(>440k atoms) I don't think is a viable idea to run n independent
Hi,
You're doing a rerun from a trajectory file that probably doesn't have
velocities in it. mdrun can compute potential energies from the position
coordinates, but these other quantities can't be computed from just the
position coordinates. mdrun can't know what you're expecting to be correct,
so
Dear all,
During the calculation of interaction energy i found one
warning
WARNING: Some frames do not contain velocities.
Ekin, temperature and pressure are incorrect,
the virial will be incorrect when constraints are present.But in
the quilibration step the temp and
Hi Justin,
Thank you for your response. In my case the cost of increasing simulation
box is very large. I have already tried it by keeping distance between the
periodic images of the macromolecule up to 50 Angstrom. Could you suggest
me any other option to do this. In Gromacs, rotation around pivot
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