Hi Rinu,
There's a suggested workflow on the Gromacs site. 'nojump' goes before
'center' because the centering may add a shift that messes up the jumps.
'whole' doean't actually change anything, so it can be used anytime before
fitting, which messes up the PBC.
Cheers,
Tsjerk
On Sep 19, 2014 6:2
hello Tsjerk Wassenaar
can we use both command pbc whole and pbc nojump and in which stage of
simulation we have to use it because in the tutorial it is written
before center the protein in the box
thanks in advance
On Thu, Sep 18, 2014 at 9:40 PM, Tsjerk Wassenaar wrote:
> Hi Prathiba,
>
> Wi
Hi all,
I run gromacs 4.6 on 5 nodes(each has 16 CPU cores and 2 Nvidia K20m)
and 4 nodes in the following ways:
5 nodes:
1. Each node has 8 MPI processes, and use one node as PME-dedicated node
2. Each node has 8 MPI processes, and use two nodes as PME-dedicated nodes
3. Each node has 4 MPI p
Hi all,
In the page 34 of the manual:
The Verlet cut-off scheme is implemented in a very efficient fashion
based on clusters of particles.
The simplest example is a cluster size of 4 particles. The pair list is
then constructed based on
cluster pairs.
I want to know on what condition will 4 par
Dear David, Thanks for the reply! I was wondering if you have had the same issue with this force field, such that you could only use one domain for all the SWM4-NDP calculations?Knowing that I could only use one MPI rank, is there a way to get the calculation work on two nodes? One of my systems ha
Hi Mark, Thanks for your reply email.- 원본 메일 -보낸사람 : Mark Abraham 받는사람 : Discussion list for GROMACS us 받은날짜 : 2014년 9월 18일(목) 21:26:48제목 : Re: [gmx-users] Problem with: Shell particles are not implemented with domain deOn Thu, Sep 18, 2014 at 2:01 PM, Kester Wong wrote:
> Dear
Dear David, Justin, Mark and all, Many thanks for your feedback, that really helped clarify a lot of the questions I had. - 원본 메일 -보낸사람 : Justin Lemkul 받는사람 : 받은날짜 : 2014년 9월 18일(목) 21:26:41제목 : Re: [gmx-users] Problem with: Shell particles are not implemented with domain deOn 9/18
Some scaling results that might be of interest to some people.
Machine = Barcoo @ VLSCI
2.7GHz Intel Sandybridge cores
256GB RAM
16 cores per node
Mellanox FDR14 InfiniBand switch
Systems = water and octanol only with GROMOS53a6
# Atoms = 10,000 to 1,000,000
Comparison Group versus Verlet neigh
Thank you Mark for the detailed response.
Knew there had to be a good reason for it :)
> ... because the only way such documentation might stay up to date is to
> generate it from the code. We'd like to make the documentation
Easier things are to do, more likely to stay up to date, and more time
Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm,
which doesn’t make any sense (because i presumed that at this distance there
must be a steric ef
On 9/18/14 1:11 PM, David van der Spoel wrote:
On 2014-09-18 14:26, Justin Lemkul wrote:
On 9/18/14 8:01 AM, Kester Wong wrote:
Dear gromacs users,
Has anyone experienced a problem with running polarisable water model
SWM4-NDP
with the following warning: Shell particles are not implemente
On 9/18/14 1:51 PM, Yunlong Liu wrote:
Hi Justin,
I built Gromacs 5.0.1 but it doesn't work even with pdb2gmx. Since my protein
is patched with -NH3+ and -COO- at the N-terminus and C-terminus. I used -ter
flag.
But the program cannot recognize the terminus and returns error.
This probab
On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:
Dear gromacs users,
In order to measure the interactions between a Protein with respect to a
mixture solvent solution (glycerol-water) i’m trying to measure the RDF
between the protein with respect to the C and O atoms of Glycerol respective
Dear gromacs users,
In order to measure the interactions between a Protein with respect to a
mixture solvent solution (glycerol-water) i’m trying to measure the RDF
between the protein with respect to the C and O atoms of Glycerol respectively.
By now i have measured g(r) between:
Protein - Gl
Hi Justin,
I built Gromacs 5.0.1 but it doesn't work even with pdb2gmx. Since my protein
is patched with -NH3+ and -COO- at the N-terminus and C-terminus. I used -ter
flag.
But the program cannot recognize the terminus and returns error.
I switched back to the Gromacs 5.0-rc1. It works fine wi
On 2014-09-18 14:26, Justin Lemkul wrote:
On 9/18/14 8:01 AM, Kester Wong wrote:
Dear gromacs users,
Has anyone experienced a problem with running polarisable water model
SWM4-NDP
with the following warning: Shell particles are not implemented with
domain
decomposition?
Out of curiosity,
Hi Prathiba,
With -pbc nojump, an atom that jumps from one side to the box to the other
is reset, so the trajectory is made continuous. If the molecule is broken
and you remove jumps, the molecule will stay broken.
With -pbc whole, the molecule is made whole, which means that the atoms are
shifte
On 9/18/14 11:51 AM, pratibha kapoor wrote:
Hi users
I have question regarding difference between pbc whole and pbc nojump
options using trjconv. Please help me understand this.
Have you read trjconv -h yet?
-Justin
--
==
Justin A. Lemkul,
Hi users
I have question regarding difference between pbc whole and pbc nojump
options using trjconv. Please help me understand this.
--
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Dear Alexander,
As Vitaly has already suggested, it is possible to simulate growth.
I'd, on the other hand, underline what Micholas has said.
It may take some planning. Here are a few ideas how to do it.
1. If you are simulating cleaving/forming bonds, the topology would change
which is difficult
On Thu, Sep 18, 2014 at 12:02 AM, Dallas Warren
wrote:
> Can I put in a request to have the full list of GROMACS commands/scripts,
> along with their help text, added back to the end of the manual? Or at
> least have a separate PDF available?
>
I doubt it will come back in its old form...
> W
On 9/17/14 6:02 PM, Dallas Warren wrote:
Can I put in a request to have the full list of GROMACS commands/scripts, along
with their help text, added back to the end of the manual? Or at least have a
separate PDF available?
What was the reason for removing that section?
Over the years I hav
On 9/17/14 6:54 PM, Yunlong Liu wrote:
Hi,
I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my
membrane protein system with POPC membrane and TIP3P water in VMD. Then I used
gmx pdb2gmx to build gromacs topology files.
My force field is charmm22* and it contains
On 9/17/14 10:07 PM, Kester Wong wrote:
That would be great Justin, I look forward to using the new Drude tool.
I have registered but could not upload a file to the User Contribution page.
See the note on the homepage about getting permission to modify pages:
http://www.gromacs.org/
-Ju
On 9/18/14 4:42 AM, Sathish Kumar wrote:
Hai
I run the umbrella sampling with the help of tutorial of
justinIn my system rna is binding with gold nanoparticle...to find out
the binding energy i run the umbrella sampling using the space 0.2 nm and i
got total 59 configurations, each
On 9/18/14 4:53 AM, Ujwala Patil wrote:
Hello I am doing simulation of dioxane+ water system
during energy minimization i got error
Too many LINCS warnings (1337)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAX
On Thu, Sep 18, 2014 at 2:01 PM, Kester Wong wrote:
> Dear gromacs users,
>
>
> Has anyone experienced a problem with running polarisable water model
> SWM4-NDP with the following warning: Shell particles are not implemented
> with domain decomposition?
>
That means what it says - you can't have
On 9/18/14 6:38 AM, RINU KHATTRI wrote:
hello
i am also facing the same problem i worked on the protein complex
(popc ) but once again i am using same procedure its gives error even
i changed .mdp file parameters
Changed to what? From what?
after running it gives 61%
mdrun
grompp -f npt.m
On 9/18/14 8:01 AM, Kester Wong wrote:
Dear gromacs users,
Has anyone experienced a problem with running polarisable water model SWM4-NDP
with the following warning: Shell particles are not implemented with domain
decomposition?
Out of curiosity, what is the source of your SWM4-NDP topolog
I should clarify, If you are not concerned with the formation of covalent
bonds, you can simulate growth, to some extent. Protein aggregation, for
instance, can be studied with MD because of this; so if you are only interested
in the early assembly, and not with electronic structure/covalent bon
Dear gromacs users, Has anyone experienced a problem with running polarisable water model SWM4-NDP with the following warning: Shell particles are not implemented with domain decomposition?The md.log also stated the following: Number of hardware threads detected (12) does not match the number repor
Hi JIom,
There is no check for correspondence of atoms. Honestly, you don't want to
have programs trying do that kind of thinking for you unthinkingly. You
should make sure that the atom order in the reference structure corresponds
to the other structure. Your RMSD may seem reasonable though, beca
hello
i am also facing the same problem i worked on the protein complex
(popc ) but once again i am using same procedure its gives error even
i changed .mdp file parameters
after running it gives 61%
mdrun
grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
mdrun -nt 4 -
For now I created a redmine issue:
http://redmine.gromacs.org/issues/1598, you can track the status
there.
--
Szilárd
On Thu, Sep 18, 2014 at 10:28 AM, Michael Brunsteiner wrote:
>
> Dear Szilard,
> thanks for your reply!
> one more question ... you wrote that SIMD optimized RB-dihedrals might g
Hello I am doing simulation of dioxane+ water system
during energy minimization i got error
Too many LINCS warnings (1337)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better
Hai
I run the umbrella sampling with the help of tutorial of
justinIn my system rna is binding with gold nanoparticle...to find out
the binding energy i run the umbrella sampling using the space 0.2 nm and i
got total 59 configurations, each configuration was run for 5 ns. The
profile is
Dear Szilard,
thanks for your reply!
one more question ... you wrote that SIMD optimized RB-dihedrals might get
implemented
soon ... is there perhaps a link on gerrit.gromacs.org that i can use to follow
the progress there?
cheers
michael
===
Why be happy when
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