Hi there,
I'm pretty sure it's not a feature but a bug which I've faced in the GMX
versions 2018.7, 2019.5 an 2020.
When I try to calculate RMSD values for a protein system including a
catalytic magnesium ion "Mg" using the command
gmx rms -s mol.pdb -f mol.xtc -f2 mol.xtc -o mol-rmsd.xvg
and,itp file o make things work. I hope this helps someone out
there struggling with similar problems.
Vedat
Am 28.08.19 um 14:30 schrieb Mark Abraham:
> Hi,
>
> The answer is still the same - if gbsa.itp has the right contents, is it
> being included at the right time?
>
> Ma
Sorry, typo: "I can NOT get my system grompped" ...
Am 28.08.19 um 12:03 schrieb Vedat Durmaz:
> Hi everybody,
>
>
> After 7 years I'm trying to do some implicit solvent simulations of
> protein-ligand systems again using Gromacs/Amber and running into the
>
Hi everybody,
After 7 years I'm trying to do some implicit solvent simulations of
protein-ligand systems again using Gromacs/Amber and running into the
same issue as before:
GB parameter(s) missing or negative for atom type 'N3'
GB parameter(s) missing or negative for atom type 'H'
GB
hi guys,
according to the gromacs installation instructions (i think a saw it
here:
http://manual.gromacs.org/documentation/2018/install-guide/index.html)
it could make sense to compile gromacs mdrun independently from the
other gromacs tools in order to have a cross-compiled installation
hi everybody,
i'm working on an ubuntu 16.04 system with gromacs-openmpi (5.1.2) installed
from the ubuntu repos. everything works fine when i submit job.slurm using
sbatch where job.slurm roughly looks like this
-
#!/bin/bash -l
#SBATCH -N 1
#SBATCH -n 24
#SBATCH -t
Am 07.09.2017 um 21:10 schrieb Justin Lemkul:
>
> On 9/7/17 10:29 AM, Vedat Durmaz wrote:
>> i really appreciate this pretty informative answer. and do you also know,
>> what the infix "n254" or "n2" stands for?
> Node ID.
>
>> what i found st
tin Lemkul:
>
> On 9/6/17 5:55 AM, Vedat Durmaz wrote:
>> hi guys,
>>
>> from time to time i'm faced with GMX output files during MD called, e.g. in
>> the current case:
>>
>> step8164372b_n254.pdb
>> step8164372b_n2.pdb
>> step8164372c_n254.pdb
written to the pdb files
and what does the file name tell me?
any hint is appreciated.
many thanks,
vedat durmaz
--
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
Takustrasse 7
14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz
d input for g_mmpbsa, if echo or < wrote:
hi again,
3 answers are hidden somewhere below ..
Am 28.10.2015 um 15:45 schrieb Mark Abraham:
Hi,
On Wed, Oct 28, 2015 at 3:19 PM Vedat Durmaz <dur...@zib.de> wrote:
Am 27.10.2015 um 23:57 schrieb Mark Abraham:
Hi,
On Tue, Oct 27, 2015
hi again,
3 answers are hidden somewhere below ..
Am 28.10.2015 um 15:45 schrieb Mark Abraham:
Hi,
On Wed, Oct 28, 2015 at 3:19 PM Vedat Durmaz <dur...@zib.de> wrote:
Am 27.10.2015 um 23:57 schrieb Mark Abraham:
Hi,
On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz <dur...@zib.
Am 27.10.2015 um 23:57 schrieb Mark Abraham:
Hi,
On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz <dur...@zib.de> wrote:
hi mark,
many thanks. but can you be a little more precise? the author's only
hint regarding mpi is on this site
"http://rashmikumari.github.io/g_mmpbsa/How-
hi guys,
I'm struggling with the use of diverse gromacs commands on a Cray XC30
system. actually, it's about the external tool g_mmpbsa which requires
user action during runtime. i get similar errors with other Gromacs
tools, e.g., make_ndx, though, i know that it doesn't make sense to use
mpbsa/Usage.html
Mark
On Tue, Oct 27, 2015 at 10:10 PM Vedat Durmaz <dur...@zib.de> wrote:
hi guys,
I'm struggling with the use of diverse gromacs commands on a Cray XC30
system. actually, it's about the external tool g_mmpbsa which requires
user action during runtime. i get similar errors
hi guys,
sorry for disturbing!
the pc of a student here has ubuntu 14.04 installed on it along with the
gromacs version 4.6.5 debian/ubuntu binaries from the ubuntu repositories.
when we start mdrun, we get an german error message saying:
ungültiger maschinenbefehl (something like invalid
?
vedat
Am 25.09.2014 um 15:28 schrieb Mark Abraham:
On Thu, Sep 25, 2014 at 12:16 PM, Vedat Durmaz dur...@zib.de wrote:
hi guys,
sorry for disturbing!
the pc of a student here has ubuntu 14.04 installed on it along with the
gromacs version 4.6.5 debian/ubuntu binaries from the ubuntu
Acceleration most likely to fit this hardware: SSE4.1
Acceleration selected at GROMACS compile time: SSE4.1
Am 25.09.2014 um 13:36 schrieb Mirco Wahab:
On 25.09.2014 12:16, Vedat Durmaz wrote:
gromacs version 4.6.5 debian/ubuntu binaries from the ubuntu
repositories.
when we start mdrun, we get
i've recieved your email concernig energy minimisation step in protein
lipid simulation already 3 times ..
maybe you've deactivated the delivery of mails? if so, do the following:
go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
and log in where it says To unsubscribe
have sent with out title has appeared.
regards
Suriyanarayanan
On Thu, Jun 12, 2014 at 3:14 PM, Vedat Durmaz dur...@zib.de
mailto:dur...@zib.de wrote:
i've recieved your email concernig energy minimisation step in
protein
lipid simulation already 3 times ..
maybe you've
i've recieved your email concernig energy minimisation step in protein
lipid simulation already 3 times ..
maybe you've deactivated the delivery of mails? if so, do the following:
go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
and log in where it says To unsubscribe
hi justin gmx-users,
meanwhile i had understood that the reference distance in the speconds file is
not an upper boundary for possible bonds but the distance itself +/-x. i should
have read the manual with more attention before writing to the list.
thanks again,
vedat
dear gmx
dear gmx users/team,
i've defined some simple residues (5 monomeric units) in aminoacids.rtp,
residues.dat and aminoacids.hdb that i want to use for the modelling of
small polymers. the polymer may be highly bifurcated due to a branching
T piece among the monomer units.
all possible
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