Hi Melsa,
I think that your problem could belong to the fact that in the .xtc file you do
not write all the frames, but every n-steps. Thus, the last frame of your xtc
file is a multiple of n-step (a discrete value) and not necessary the real last
one, that for sure is represented by md300.gro.
Dear Gromacs users!
I'd like to use g_cluster utility to cluster a big set of models produced
by Modeller as the result of the refirement of some parts of my protein. In
this case all structures differs only in the conformation of 1 longest loop
(~ 30 amino acids including 2 disulphide bridges)
Hi James,
The first part is just conformational clustering, for which you can use
g_cluster. The easiest is then to collect the structures belonging to the
different clusters in different files (which g_cluster can do), which you
process separately to extract those properties you're interested
On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com
wrote:
Hi
In general, virtualization will always have an overhead, but if done
well, the performance should be close to that of bare metal. However,
for GROMACS the ideal scenario is exclusive host access (including
Dear Group,
I have defined different specific groups in the index.ndx file. My problem is
that if I try to add a new group, the old ones are disappearing. Should it be
like this?
Yours sincerely,
Ingrid Pettersson
_
Ingrid Pettersson, PhD
Principal Scientist
On 7/25/14, 7:35 AM, Cyrus Djahedi wrote:
There is something else. I also tried using mk_angndx to generate an index file prior to
using g_angle by: mk_angndx -s C0.tpr -type angle
It generates a lot of different angle group that I can not identify. Each line
in the index-file has 9 atoms in
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files by hand and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because i need
to learn GROMACS). I have learnt on
Dear Gromacs users,
I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential
parameters already defined in OPLSAA forcefield, so I wanted to know if I want
to add FE+3 in my simulation, then the LJ parameters for it will be different
from that of Fe+2 or same?
I thought it
On 7/25/14, 7:39 AM, #SUKRITI GUPTA# wrote:
Dear Gromacs users,
I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential
parameters already defined in OPLSAA forcefield, so I wanted to know if I want
to add FE+3 in my simulation, then the LJ parameters for it will be
On 7/25/14, 7:43 AM, Tamas Karpati wrote:
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files by hand and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because
Thank you for the help. It works fine.
BR Ingrid
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: 25. juli 2014 13:36
To: gmx-us...@gromacs.org
Subject: Re:
Dear Gromacs users,
I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential
parameters already defined in OPLSAA forcefield, so I wanted to know if I want
to add FE+3 in my simulation, then the LJ parameters for it will be different
from that of Fe+2 or same?
I thought it
Use make_ndx -f *.gro -n old_index.ndx -o old_index.ndx
On Fri, Jul 25, 2014 at 4:53 PM, INPE (Ingrid Viveka Pettersson)
i...@novonordisk.com wrote:
Dear Group,
I have defined different specific groups in the index.ndx file. My problem
is that if I try to add a new group, the old ones are
Dear Justin,
Thank you for your quick answer.
Same with GROMACS-4.6.6: core-to-shell distance
must be 0 to not crash. My crystal is expected to be polarized
(metallic and oxygen sites are the victims of this model).
The *.mpd file being used is:
# nstcalcenergy = 1 ; 4.6.6 claims this
Dear Justin,
Thanks for your reply. Then it there any relation between charge density (for
same element) and lj parameters e.g. for higher charge vander waals radius is
smaller? Or are lj parameters randomly selected just to satisfy physical
behavior of the ions?
Regards
Sukriti
Sukriti
On 7/25/14, 8:21 AM, #SUKRITI GUPTA# wrote:
Dear Justin,
Thanks for your reply. Then it there any relation between charge density (for
same element) and lj parameters e.g. for higher charge vander waals radius is
smaller? Or are lj parameters randomly selected just to satisfy physical
On 7/25/14, 8:10 AM, Tamas Karpati wrote:
Dear Justin,
Thank you for your quick answer.
Same with GROMACS-4.6.6: core-to-shell distance
must be 0 to not crash. My crystal is expected to be polarized
Does your topology specify the proper intramolecular exclusions? What is(are)
the
Dear GROMACS Users,
I have a problem when running genbox_mpi.
Below is information from the console.
[lswiercz@nostromo ~/gromacs]$ srun --nodes 1 genbox_mpi -cp
1AKI_newbox.gro -cs spc216.gro -p topol.top -o solvated.gro
srun: job 5026 queued and waiting for resources
srun: job 5026 has been
On 7/25/14, 11:20 AM, lswierczewski . wrote:
Dear GROMACS Users,
I have a problem when running genbox_mpi.
Below is information from the console.
[lswiercz@nostromo ~/gromacs]$ srun --nodes 1 genbox_mpi -cp
1AKI_newbox.gro -cs spc216.gro -p topol.top -o solvated.gro
srun: job 5026 queued
On 7/25/14, 11:22 AM, Tamas Karpati wrote:
Dear Justin,
Does your topology specify the proper intramolecular exclusions? What
is(are) the molecule(s)?
No bonds, no exclusions. The whole crystal is modelled by ions
interacting via forces of the Coulomb and Buckingham types.
In fact, there
Dear Justin,
Does your topology specify the proper intramolecular exclusions? What
is(are) the molecule(s)?
No bonds, no exclusions. The whole crystal is modelled by ions
interacting via forces of the Coulomb and Buckingham types.
In fact, there is an X-Y-X angle force type which does have an
Dear Justin,
Thanks for your educational answers.
Coulombic interactions fail at short distances; you probably need to apply
I was afraid of that... somehow removing shells from the cores in the
initial structure have let it functionally work (with not yet
reasonable results).
Thole
On Fri, Jul 25, 2014 at 12:33 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com
wrote:
Hi
In general, virtualization will always have an overhead, but if done
well, the performance should be close to that of bare metal.
They report the time since the step that the timers were reset. The log
file will note this event. Whether load is balanced by then/ever depends on
the load.
Mark
On Jul 25, 2014 7:31 PM, Sikandar Mashayak symasha...@gmail.com wrote:
Thanks Szilárd.
I am bit confused about the -resethway or
Got it! Thanks Mark.
On Fri, Jul 25, 2014 at 10:41 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
They report the time since the step that the timers were reset. The log
file will note this event. Whether load is balanced by then/ever depends on
the load.
Mark
On Jul 25, 2014 7:31 PM,
On 7/25/14, 12:40 PM, Tamas Karpati wrote:
Dear Justin,
Thanks for your educational answers.
Coulombic interactions fail at short distances; you probably need to apply
I was afraid of that... somehow removing shells from the cores in the
initial structure have let it functionally work
On 7/25/14, 4:17 PM, Seyyed Mohtadin Hashemi wrote:
On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi haa...@gmail.com
wrote:
Hi everyone,
I'm having a very weird problem with GROMACS 4.6.6:
I am currently testing out GPU capabilities and was trying to compile
GROMACS with CUDA
On Fri, Jul 25, 2014 at 3:17 PM, Seyyed Mohtadin Hashemi haa...@gmail.com
wrote:
On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi haa...@gmail.com
wrote:
Hi everyone,
I'm having a very weird problem with GROMACS 4.6.6:
I am currently testing out GPU capabilities and was trying to
Dear GROMACS Users:
Would you please let me know how to calculate/extract the electrostatic
forces and van der waals forces of an ionic liquid structure in GROMACS?
Which GROMACS command should I use? g_enemat? g_potential?
Thanks a lot!
Andy
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