Hi,
You're running 2016.x which had a bug, not the 2018.x you thought you were
using. Use GMXRC or your cluster's modules to select the version you want
to use in the terminal or script that you want to use.
Mark
On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh
wrote:
> What kind of error is
On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:
I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.
Can I get example of
This is make check reuslt
100% tests passed, 0 tests failed out of 27
Label Time Summary:
GTest = 1.24 sec*proc (18 tests)
IntegrationTest = 5.93 sec*proc (2 tests)
MpiIntegrationTest
Hi,
If you have a reason to have to use 2016.x, then please get the latest
version (which is always advisable when starting new work) because this
issue is fixed there. You also don't have to run energy minimization on
GPUs, so you could just append -nb cpu to your mdrun command line to avoid
the
Currently I am using only gromacs16.5. As this have *"PLEASE NOTE* that the
current versions do support lone pair construction on halogens, however the
current construction is only compatible with GROMACS-2016.x and by using
gmx grompp -maxwarn 1 to override the warning about lone pair
I have seen this in Gromacs manual.
[ virtual_sites2 ]
; Site fromfunct a
5 1 2 1 0.7439756
for type 3 like this:
[ virtual_sites3 ]
; Site from funct a b
5
Thank You Sir.
Again installed gromacs2016.6 (final version from gromacs2016.x).
Throwing same error(HtoD cudaMemcpyAsync failed: invalid argument)
. Its running on CPU, but not on GPU. Work of 3 days will take 15 days.
Already completed simulation for other complexes. This complex creating
On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
Do I have to add vsite3 information from unk.itp to system.top files?
That directive belongs in the topology to which it corresponds. If it is
in unk.itp, then it is already in system.top. You don't need to include
anything else.
-Justin
Den 2019-08-26 kl. 20:53, skrev Najla Hosseini:
Dear David,
Hope you are doing well.
I am Gromacs user and I need to change the partial charge of molecules
in force field or itp file as a function of distance during the run in
Gromacs. Is it possible? How I should do that?
Please pose your
Hi,
You should follow the error message instructions "... they should not have
the same chain ID as the adjacent protein chain" which you know is that X.
Make the protein have a different chain ID from the rest.
Mark
On Mon, 26 Aug 2019 at 19:27, Ayesha Fatima
wrote:
> Dear Justin,
> Thank
I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.
Can I get example of any topology file where these kind of construction've
Dear Justin,
Thank you for your earlier response. I opened the file in vmd and it
returned me with a 3 letter residue name and an X identifier for the whole
molecule.
CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1
ATOM 1 C3 CHL X 1 -1.678 2.702 17.328
What kind of error is this. Previously Gromacs 2018.4 version was running
fine using GPU. But Now this error I am getting.
_
gmx mdrun -v -deffnm em
:-) GROMACS - gmx mdrun, 2016.5 (-:
Hello gromacs users,
I saw the following error for a modified residue I added though I edited all
necessary files including PDB. I also read the gromacs documentation on this
error.
Residue XXX not found in residue topology database.
Any hints on what might be happening?
Many thanks,
Neena
On 8/26/19 8:27 PM, Neena Susan Eappen wrote:
Hello gromacs users,
I saw the following error for a modified residue I added though I edited all
necessary files including PDB. I also read the gromacs documentation on this
error.
Residue XXX not found in residue topology database.
Any
Dear users,
I am trying to perform a simulation with a protein which contains two
nickel atoms in the active site.
When using the pdb2gmx command the following error appears:
'NI' not found in residue topology database
I have edited the ions.itp file in the force field directory used (opls)
Hi,
All versions of icc requires a standard library from an installation of
gcc. There are various dependencies between them, and your system admins
should have an idea which one is known to work well in your case. If you
need to help the GROMACS build find the right one, do check out the GROMACS
Dear All,
I have come across another issue
When i want to use opls itp for cholesterol, it gives me this error " Fatal
error:
Residue 'OL' not found in residue topology database"
It does not take CHOL as the residue name as given below
[ atoms ]
; nr type resnr residue atom cgnr
Hi,
>
> Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS
> Tutorial ) for my file which is protein-ligand complex.
> The pulling force was in Y direction. when Umbrella sampling finished,
> "Wham" couldn't analysis the data because wham is in z direction.what
> should I
Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS
Tutorial ) for my file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for
Dear all,
I want to restrain some water in a big cluster where the water can move freely
in the cluster but they cannot move out of the cluster. How can I do to
implement the restrain?
Thank you very much!
Sincerely,
Wentian
--
Institute of Theoretical and Computational
On 8/26/19 5:41 AM, wtzou wrote:
Dear all,
I want to restrain some water in a big cluster where the water can move freely
in the cluster but they cannot move out of the cluster. How can I do to
implement the restrain?
Check the manual for flat-bottom restraints.
-Justin
--
On 8/26/19 7:04 AM, Ayesha Fatima wrote:
Dear All,
I have come across another issue
When i want to use opls itp for cholesterol, it gives me this error " Fatal
error:
Residue 'OL' not found in residue topology database"
It does not take CHOL as the residue name as given below
That suggests
Hi,
I am trying to compile Gromacs-2019.3 at our HPC cluster. I successfully
compiled the single and double precision versions, but it’s producing error for
GPU support. (The error message is pasted below)
I am using Intel/2018 update 4 and CUDA/10.0. The base gcc version is 4.8.5.
Using MKL
Hi,
you can also use the pullf output for WHAM (option -if), this may be easier.
Cheers, Jochen
Am 26.08.19 um 12:59 schrieb Negar Parvizi:
Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS
Tutorial ) for my file which is protein-ligand complex.
The pulling force
On 8/26/19 12:04 PM, Edjan Silva wrote:
Dear users,
I am trying to perform a simulation with a protein which contains two
nickel atoms in the active site.
When using the pdb2gmx command the following error appears:
'NI' not found in residue topology database
I have edited the ions.itp
Do I have to add vsite3 information from unk.itp to system.top files?
-maxwarn 1 flag I checked in gromacs 16 version and it's running there.
On Mon, 26 Aug 2019, 00:58 Justin Lemkul, wrote:
>
>
> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > Yeah! I have read that.
> >
> > uses -maxwarn
27 matches
Mail list logo
