Dear Justin and Dallas,
Thanks for your answers. I am so confused. I am beginner in MD simulation
of lipid + small molecule.
'' There are far better options for lipids than the old Berger parameters
used in the tutorial. I wrote the tutorial in 2008 and it reflected a
common protocol at the time
Could you help me deal with GC-AdResS approach implemented in Gromacs?
Recently I learned about the GC-AdResS approach implemented in Gromacs
(https://www.researchgate.net/publication/326361115_Adaptive_resolution_molecular_dynamics_technique_Down_to_the_essential
et.al.) I downloaded and
Have you tried running stress test benchmarks for CPU and GPU? Or just
looking up any similar issues reported by other users of your MB and CPU
models?
Sudden shutdowns at high load are generally caused by power or cooling
failure. Or both, like CPU or GPU VRMs overheating, since they're
Hello,
I am experimenting with GROMACS 2020. I have compiled the mpi threaded
version and am using the new settings
(GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as
suggested on at the following link:
You need to use the same forcefield.
Since you are using ATB to generate the topology for your small molecule,
then it stands to reason that you then should use ATB for the lipid
molecule.
Search ATB, I'm pretty sure the various lipids will already be there, and
suspect they will be some that
Dear Gromacs users
I am restraining three dihedral angles between atoms of two
different residues. when I measure it using the following command:-
gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of
trans.xvg
I am getting one of my dihedrals graphs as mentioned in the link.
Dear Gromacs users
I am restraining three dihedral angles between atoms of two
different residues. when I measure it using the following command:-
gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of
trans.xvg
I am getting one of my dihedrals graphs as mentioned in the link.
Hi Kunal,
Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix Sport
LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD 860 EVO 2TB
SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler.
It looks like the reason of my PC shut down is lying in the
Hi Dallas,
The temperature of CPU is fine, it is less than 59C. Mdrun started work
properly after I changed Bios settings to the default settings.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Dallas Warren
Sent: Monday, March 2, 2020
Hello,
If you try an updated version, please try an actually recent one, either
2019.6 or the 2020 release.
If you could provide us with some error or log messages we might be able
to find out what happened there.
Cheers
Paul
On 02/03/2020 16:03, Kamran Gul, M.Phil. Scholar, Institute of
Try gromacs 2019.2.
And then update your cuda and nvidia.
On Mon, 2 Mar 2020, 6:58 p.m. Kunal Dutta, wrote:
> Hello Sir,
> May I know the detailed configuration of your system.
> Sincerely,
> Kunal
>
>
>
>
> On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir
> wrote:
>
> > Hi all,
> >
> > I
Hello Sir,
May I know the detailed configuration of your system.
Sincerely,
Kunal
On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote:
> Hi all,
>
> I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but
> when I did make check, my PC turned off. I also tried to install
On 3/2/20 2:40 AM, Atila Petrosian wrote:
Hi Dallas,
thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB
server.
My system contains lipid molecules and small molecule. For lipid molecules,
Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both
of
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