Dear Gromacs users,
I'm simulation a double chain protein-ligand complex using Amber force
field. I have written parameters and generated the topology.
The energy minimization of the complex gives me the following error:
*Energy minimization has stopped, but the forces have not converged to the*
BS”D
Dear All,
The new Skylake-X CPU’s have very high core counts, and could, in theory,
take the place of a two socket 16 core Xeon system. One could create a machine
as follows:
1 x Core i9 7960X with 16 cores
2 x Geforce 1080 graphic cards,
and run a simulation with 2 MPI ranks, couplin
Any ideas?
Anders
On Fri, Oct 13, 2017 at 3:15 PM, Anders Støttrup Larsen wrote:
> Hi all
>
> I have been trying to simulate a system containing two walls and a
> slab/vacuum. During the simulation water from the slab diffuses into the
> vacuum as intended. The problem is that this causes the s
Hi,
There's no real issue there. If anything, it's simpler. With the dual
socket system it would often make no sense to extend an OpenMP region
across the sockets. That's still true if there's internal structure that
makes some cores further from others (I dunno if true for Skylake-X). You'd
still
Dear Harry,
we have several nodes with single i9 7900 decacore processors and one
gtx 1080ti each. So far they show very good performance compared with
dual 16 core xeon nodes with two K20x and even K40x cards. We reach a
performance of >40ns per day for >9 atoms with the i9 system,
compa
Dear Harry,
we have several nodes with single i9 7900 decacore processors and one
gtx 1080ti each. So far they show very good performance compared with
dual 16 core xeon nodes with two K20x and even K40x cards. We reach a
performance of >40ns per day for >9 atoms with the i9 system,
compa
Hello everyone,
It is any tool to track water molecules (or a particle in general) along
a simulation trajectory, so the final result is the pathway/streamline
of selected water molecules? It would something similar to what was done
in this paper http://pubs.acs.org/doi/abs/10.1021/bi901900s.
On 10/15/17 11:27 PM, Dilip H N wrote:
Thank you Justin Sir,
1] But how do i solve this issue..?? and make sure that pdb2gmx is not
interpreting my input as being a single chain and it's finding dissimilar
residue types..?? even i tried with gmx pdb2gmx with -ter command, but
still, i am getti
On 10/16/17 5:19 AM, Khadija Amine wrote:
Dear Gromacs users,
I'm simulation a double chain protein-ligand complex using Amber force
field. I have written parameters and generated the topology.
The energy minimization of the complex gives me the following error:
*Energy minimization has stop
On 10/16/17 7:16 AM, Yasser Almeida Hernández wrote:
Hello everyone,
It is any tool to track water molecules (or a particle in general)
along a simulation trajectory, so the final result is the
pathway/streamline of selected water molecules? It would something
similar to what was done in th
Dear Hess,
I have two questions about the usage of the PME-User in coulombtype parameter.
I didn't get replies from the GMX-USER mail list. Could you please give some
details? The forwarded mail is the two questions I asked.
Thanks for your help.
Yu
-Original Messages-
From: "Du, Yu"
Hi All,
I think that there is a bug in "gmx convert-tpr", as I understand that
"gmx dump" dumps wrong atom types and some wrong numbers when working
with some modified tpr files. I attach clear instructions on how to get
the bug, as well as two input files and the faulty .trp.
I found the pro
BS”D
Dear Bernard,
Thank you for your reply and info. Our experience with a second graphics
card (when coupled with the appropriate number of cores) is that we garner
close to a 100% performance gain. We have access to nodes on a cluster with 16
cores (2 x E5-2630 v3) + 1 K80 (dual gpu on
Dear Harry,
you are right for the dual xeon 16 core setup you (and we) use, but for
the single core i9 setup we made the experience, that we only gained
between 5-10% of performance by adding a second gpu. This was what I was
hinting here...
Best Bernhard
Am 16/10/17 um 14:56 schrieb Harry
Dear Gromacs Users,
I have a question about the gmx traj in order to calculate the force
components.
I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
-af force_all_z_l9.xvg -z yes
It produced "force_all_z_l9.xvg" file. In the file, there are four columns.
The first
On 10/16/17 9:36 AM, Chang Woon Jang wrote:
Dear Gromacs Users,
I have a question about the gmx traj in order to calculate the force
components.
I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
-af force_all_z_l9.xvg -z yes
It produced "force_all_z_l9.xvg" file
On Mon, Oct 16, 2017 at 2:56 PM, Harry Mark Greenblatt
wrote:
> BS”D
>
> Dear Bernard,
>
> Thank you for your reply and info. Our experience with a second graphics
> card (when coupled with the appropriate number of cores) is that we garner
> close to a 100% performance gain. We have access
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, Lab
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 -ign
My guess would be that when you thought ran it with the increased box
size coordinate file, you actually used the original coordinate file.
FYI
http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_eleme
Dear gromacs users
I would like to do dPCA for my 100ns trajectory. When see in the gromacs
tutorial I could not create the covar.ndx file. My peptide is 20 residues
length. I made .ndx file for dihedral angles and after generating the
dangle.trr file. But here I have one problem, to generate the
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