Dear all,
I ran an energy minimization and molecular dynamics on biotin in a box of
water. The EM ran fine however the MD output shows biotin broken into
pieces from the start to the end.
Did the MD run correctly? I used the trjconv with the -pbc nojump flag,
so I am not sure why it is showing
On 3/19/15 9:25 PM, Ming Tang wrote:
Dear all,
I had a problems with parallel calculation of a implicit solvent problem. My
gromacs is compiled with mpi, so technically, I run mdrun_mpi for my
simulation. I am calling 12 cpus for my simulation and started 12 treads.
When I put a limited
On 3/20/15 9:00 AM, Jessica Leuchter wrote:
Dear All,
I would like to add dihedral restraints to 10 residues in my topology
file using the newest version of gromacs. I have done the
following(see below) to my topology file. And this is the *grompp
command* I am using: gmx grompp -f ions.mdp
Dear All,
I would like to add dihedral restraints to 10 residues in my topology
file using the newest version of gromacs. I have done the
following(see below) to my topology file. And this is the *grompp
command* I am using: gmx grompp -f ions.mdp -c 1AKI_solv.gro -p
topol.top -o ions.tpr. But I
Dear all,
I am very new to Gramacs (switching from AMBER in order to use GROMOS and
CHARMM force fields for carbohydrates) and need some help in preparing
topologies. I had a brief look in the tutorials and gromacs force field
files but I could not find any useful information about using GROMOS
Hello all,
I have a stupid question :
I would like to use gangle (v5.0.4) with the following command line
gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n
paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav test_angle.xvg
-b 39000 -e 4 test_angle.txt
On 3/20/15 11:51 AM, mish wrote:
Dear all,
I am very new to Gramacs (switching from AMBER in order to use GROMOS and
CHARMM force fields for carbohydrates) and need some help in preparing
topologies. I had a brief look in the tutorials and gromacs force field
files but I could not find any
On 3/20/15 11:49 AM, ABEL Stephane 175950 wrote:
Hello all,
I have a stupid question :
I would like to use gangle (v5.0.4) with the following command line
gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n
paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav
On 3/20/15 1:13 PM, Yunlong Liu wrote:
Hi,
I am running my protein with two ligands. Both ligands are small molecules like
ATP. However, my simulation performance drops a lot by adding this two ligands
with the same set of other parameters.
Previously with ligands, I have 30 ns/day with
On 3/20/15 1:16 PM, Marcelo Depólo wrote:
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
Install it, sure, but from where? You provided a DOI to the article, which
makes
Many thanks :). It should be enough to start.
Best,
Mish
On Fri, Mar 20, 2015 at 6:32 PM, Thomas Piggot t.pig...@soton.ac.uk wrote:
Hi,
You can download the parameters from:
http://dqfnet.ufpe.br/biomat/Software_files/GROMOS-53A6glyc.tar
I have used them and they seem to perform fine.
Hi,
I am running my protein with two ligands. Both ligands are small
molecules like ATP. However, my simulation performance drops a lot by
adding this two ligands with the same set of other parameters.
Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But
now I can only gain
On 3/20/15 12:30 PM, mish wrote:
Many thanks. I know parameters are available in literature but my question
was how to use them in GROMACS. Now, I can see different residue names
(e.g AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM).
I think I will need to edit input pdb
From article to topology would be time taking and also more chances of
mistakes. Carbohydrates are quite important class of biomolecules and they
should be available in usable form somewhere :)
On Fri, Mar 20, 2015 at 6:21 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/20/15 1:16 PM, Marcelo
2015-03-20 14:21 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 3/20/15 1:16 PM, Marcelo Depólo wrote:
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
Install it, sure, but
Hi,
You can download the parameters from:
http://dqfnet.ufpe.br/biomat/Software_files/GROMOS-53A6glyc.tar
I have used them and they seem to perform fine. They are not too
different from the previous 45A4/53A6 parameters.
Cheers
Tom
On 20/03/15 17:21, Justin Lemkul wrote:
On 3/20/15
Many thanks, Teemu
it works
Stephane
--
Message: 3
Date: Fri, 20 Mar 2015 18:05:49 +0200
From: Teemu Murtola teemu.murt...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] command line with gangle
Message-ID:
By far the simplest method is to just pass your selections as command line
arguments, without any files:
gmx gangle ... -group1 0 -group2 3
One goal for the selection implementation was that it's not necessary to
play around with complicated redirections to automate things.
On Mar 20, 2015
There is also a Modified GROMOS forcefield for glycans here:
http://dx.doi.org/10.1021/ct300479h
Cheers!
--
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
--
Gromacs Users mailing list
* Please search the
On 3/20/15 12:46 PM, mish wrote:
Many thanks. Is it possible that GROMOS parameters re also available in
similar format like CHARMM? With GROMACS there is only aminoacids.rtp
provided for recent GROMOS parameters. In general, I see only protein, dna,
rna and lipid parameters are provided in
Many thanks. I know parameters are available in literature but my question
was how to use them in GROMACS. Now, I can see different residue names
(e.g AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM).
I think I will need to edit input pdb file accordingly. However, I am still
Many thanks. Is it possible that GROMOS parameters re also available in
similar format like CHARMM? With GROMACS there is only aminoacids.rtp
provided for recent GROMOS parameters. In general, I see only protein, dna,
rna and lipid parameters are provided in code (included in /top directory)
but
As my previous email said: there is a modified GROMOS forcefield for
carbohydrated. Install it and check out which kind of modifications on
topologies you should do.
2015-03-20 13:51 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 3/20/15 12:46 PM, mish wrote:
Many thanks. Is it possible that
Recently, I've been working with colleagues to develop a new force field for
biochemical/ biophysical application - specifically proteins, RNA, DNA and
Lipids. I've been seeking a testing/ validation suite for these type of
force fields with no success.
I recently noticed this publication:
Hi Justin,
I am running this simulation on Stampede/TACC. I don't think there are other
processes running on the nodes assigned to me. This is a little weird.
Yunlong
On Mar 20, 2015, at 2:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/20/15 1:13 PM, Yunlong Liu wrote:
Hi,
I am
On 3/20/15 2:32 PM, Yunlong Liu wrote:
Hi Justin,
I am running this simulation on Stampede/TACC. I don't think there are other
processes running on the nodes assigned to me. This is a little weird.
Well, as I said, the .log files will be the definitive source of run settings
and
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