Dear all
I am involved in a project where the target systems are lipid bilayers
with and without different macromolecules embedded. In the past I did
quite a lot of MD simulations of membrane systems always removing the
COM motion of lipids and the solvent in separate groups. There are
several
Hello Dr.Lemkul
I get it.
Thank you very much for your answer.
Regards
Azadeh
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Thanks, Justin.
I will as you recommended.
The last approach was described in a book chapter for bilayer simulation.
I had difficulty to justify that approach.
Cheers,
Mohsen
On Tue, Jan 16, 2018 at 9:42 AM, Justin Lemkul wrote:
>
>
> On 1/16/18 11:37 AM, Mohsen Ramezanpour wrote:
>
>> Dear
On 1/16/18 11:37 AM, Mohsen Ramezanpour wrote:
Dear Gromacs users,
In the man page of g_density for calculation of electron density, it is
mentioned that:
"The number of electrons for each atom is modified by its atomic partial
charge."
https://linux.die.net/man/1/g_density
In some publicat
Dear Gromacs users,
In the man page of g_density for calculation of electron density, it is
mentioned that:
"The number of electrons for each atom is modified by its atomic partial
charge."
https://linux.die.net/man/1/g_density
In some publications, it seems the authors just took the atomic num
On 1/16/18 10:24 AM, kordza...@aut.ac.ir wrote:
Hi every one
I have a question
I want to obtain topology of carbon nano tube with x2top but I must determine
the value of bond strength and angle constant.
I think we have a bond carbon-carbon that stretches with a constant force for
example
Hi every one
I have a question
I want to obtain topology of carbon nano tube with x2top but I must determine
the value of bond strength and angle constant.
I think we have a bond carbon-carbon that stretches with a constant force for
example in amber force field this constant is 392459 kj /(m
I got it, Thank you very much for all the help!
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 08:46 PM
To: "gromacs.org_gmx-users";
Subject: Re: Re: Re:Can I get the fraction of solvent accessible surface
area using "g
On 1/16/18 7:46 AM, ZHANG Cheng wrote:
Hi Justin,
Thank you very much!
The legend is "Total" for the command without -surface and -output. So I feel
like if I do a division for the last columns from those two commands, I can just get the
fraction of folded/unfolded?
Strictly speaking, no,
Hi Justin,
Thank you very much!
The legend is "Total" for the command without -surface and -output. So I feel
like if I do a division for the last columns from those two commands, I can
just get the fraction of folded/unfolded?
e.g.
1.467/2.767
1.824/2.757
1.901/2.736
... ...
-
On 1/16/18 6:38 AM, MD wrote:
Hi Justin,
I got the itp and parameters of my side chain modified amino acid from
CHARMM-GUI and incorporated it into my protein structure, labeled with
HETATM. I made the atom types names consistent with charmm forcefield which
I used with gromacs and made sure o
On 1/16/18 7:02 AM, ZHANG Cheng wrote:
Hi Justin,
Thank you very much.
So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns
-surface 'group 0' -output 'group 1'
And got:
0.000 206.8651.467
0.100 232.4501.824
0.200 225.984
Hi Mark,
I implement a pseudo hard sphere potential, (LJ form potential with powers
50, 49 instead of 12,6), wiht parameter sigma and epsilon parameters and
vdW cut-off=sigma.
I used Gromacs for this and is working properly for the first step. Do you
then have an idea how big should be rlist then?
Hi Justin,
Thank you very much.
So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns
-surface 'group 0' -output 'group 1'
And got:
0.000 206.8651.467
0.100 232.4501.824
0.200 225.9841.901
... ...
So my understanding is
Hi,
Please start a new email, rather than replying to a digest and confusing
the history of the mailing list archive.
On Fri, Jan 12, 2018 at 7:05 AM Adarsh V. K.
wrote:
> In case of Protein-ligand simulation,
>
> 1) Whether all commands used in GROMACS 5.1.4 is supported in GROMACS 2018
> also
Hi,
The default changed in GROMACS 2018 - even if NVML is found, we do not link
with it by default. Use cmake -DGMX_USE_NVML=on. Be advised that you may
need to take care that the nvml library found at run time is compatible
with the CUDA version used at compilation time. That can be non-trivial t
Hi,
That depends on what model you want to implement - rlist sets the radius
within which particles/groups will be placed in the neighbour list. There's
further requirements based on the other elements of the simulation with
which it has to interact, so for user tables, the group scheme is needed,
Hi,
You still have many sources of problems (e.g. the warnings you suppressed,
the fact that your ring's atoms interact with an environment). What happens
when you minimize a capped peptide in vacuo?
Mark
On Tue, Jan 16, 2018 at 12:39 PM MD wrote:
> Hi Justin,
>
> I got the itp and parameters
Hi Justin,
I got the itp and parameters of my side chain modified amino acid from
CHARMM-GUI and incorporated it into my protein structure, labeled with
HETATM. I made the atom types names consistent with charmm forcefield which
I used with gromacs and made sure overall the parameters look decent
On 1/16/18 6:19 AM, ZHANG Cheng wrote:
Hi Alexandr,
Thank you, but it is the same with spaces between |
:(
I provided the appropriate syntax before:
http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas
-select and -output take strings that select what you want f
Hi Alexandr,
Thank you, but it is the same with spaces between |
:(
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 06:37 PM
To: "gromacs.org_gmx-users";
Subject: Re:Re: Can I get the fraction of solvent accessible su
On 16/01/2018 11:37, ZHANG Cheng wrote:
Hi Justin, thank you very much.
Sorry I still do not fully understand. I have an index file, in which the group
0 is all the residue atoms of the protein, group 1 is the first residue atoms.
I want to calculate the sasa fraction of the residue 1. The f
Hi Justin, thank you very much.
Sorry I still do not fully understand. I have an index file, in which the group
0 is all the residue atoms of the protein, group 1 is the first residue atoms.
I want to calculate the sasa fraction of the residue 1. The fraction means: the
sasa at folded state di
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