ello,
A quick question :
It is possible to save the velocities (in a trr file) for only selected atoms
"during" a simulation as we can do in case of the xtc files by using a the mdp
option compressed-x-grps?
Thanks
S
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Hi,
it is not an issue !! To resolve your problem you could simulate two bilayer in
box and insert the peptides between them.
HTH
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Message: 6
Date: Wed, 9 Nov 2016 16:07:26 +0530
From: Abhi Acharya
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-us
Dear all,
Sorry in advance if the following message does not follow the netetiquette (my
message was already post in the Martini forum) but since more gromacs users
read this mailling list than the Martini one, I think that probably some users
may help me to resolve my problem.
I am interes
Hi All,
I have a question about the reaction field approach used by GROMACS. I have
seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with the
Reaction Field approach (http://redmine.gromacs.org/issues/1400). It is
corrected in the GROMACS version than 5.0 or in lastest version
Hi Marlon,
If you change the comma into a point in the force constant values it should
work
Good luck
Hello,
I'm trying to use the amber03 ff to simulate a protein with iron clusters.
I got the right parameters from a paper but then grompp tells me:
"ERROR 1 [file clus
Hi,
Before to compute the partial charges , you have to optimize the molecule. It
may be very difficult if you have a large molecule (> 100 atoms). So for
polymers with reapeated units, it is always advisable to separate the molecule
into similar molecular blocks. It is straighforward for plu
OK thanks Yu,
I have another question how to select the water sphere center dynamically
With g_select?
S
-
Hi St?phane,
gmx gangle may be what you need.
http://manual.gromacs.org/programs/gmx-gangle.html
-Yu
2016-05-31 13:22 GMT+02:00 ABEL Stephane
Hi all,
Is there a command/tool in a gromacs to compute the angle between a vector
defined defined two atoms molecule and the normal to a sphere defined by a set
of atoms for instance water ? if yes, how
I use a version of gromacs > 5.0
Thanks
Stéphane
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Hello Shahla,
We have developed a tool for GROMACS (rtp2hdb) that can construct a hdb table
file for you with any rtp file. Please contact me contact me off list if you
are interested
Best
--
Message: 5
Date: Sat, 9 Apr 2016 08:49:05 -0400
From: Justin Lemkul
T
Indeed Justin I have tried to add the entries for the capped groups in the
Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present
in aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken
something
Stéphane
On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote
Hello again
I have noticed that in case of the amber* forcefields (in gromacs v504) the
aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not possible to
construct easily a capped AA with the pdb2gmx -ter command without using a rtp
file (and it is very painful). So does anyone ha
Hello,
When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force
field, I have the error :
Fatal error:
tpA = 53191, i= 0 in print_atoms
I have no idea what does this message mean. Could you help me?
Thanks
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Hello,
How did you construct your membrane, with CHARMM-GUI? What is the lipid? From
my experience, I have found that sometimes CHARMM-GUI does not provide a good
starting point for MD. So I would suggest you to :
- center the lipids inside the box to have no lipids that cross the box limit
a
Hello
To center your RM inside teh box you could use to successive trjconv commands
with pbc cluster and mol
in index.ndx
0 : all
1 AOT
2 water
3 AOT_Water
4 ISO
1 -- select 1 1 0 (or 2 2 0)
echo 1 1 0 | trjconv -f my_initial.xtc -s my_tpr.tpr -pbc cluster -ur compact
-center -o my_clus
Hi Anu,
You may interested by the recent work of Klauda et al. where the authors
developed a united atom force field for (phospho)lipids based on CHARMM36. It
seems to work quite well
(1) Lee, S.; Tran, A.; Allsopp, M.; Lim, J. B.; Hénin, J.; Klauda, J. B.
CHARMM36 united atom chain model f
Many thanks, Teemu
it works
Stephane
--
Message: 3
Date: Fri, 20 Mar 2015 18:05:49 +0200
From: Teemu Murtola
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] command line with gangle
Message-ID:
Content-Type: text/plain; charset=UTF-8
By
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
With
Hello,
It is not a really problem, since the water will move during the simulation
(due to the hydrophobic effect), but It may take for that all the water left
the micelle center. So I suggest you to use genbox with the following arguments
-shell or -vdwd (see the genbox manual).
An other a
Hello Bjorn
I don't know if it related to your problem, but I see a typo in our mdp file
for the pressure coupling:
Pcoupltype = isotropic ;semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 4.0 4.0
compressibility
Hello all,
I am trying to convert some GLYCAM parameters to do simulations with the
GROMACS code. In the glycam force field, several dihedral terms have negative
barrier height values, for instance, -20 in the following parameter:
Os-Cj-Cj-Ha 1 -20.00 0.0 2
Thanks for your quick and also fast (;)) reply, Carsten.
Stéphane
--
Message: 4
Date: Wed, 2 Jul 2014 10:55:45 +
From: ABEL Stephane 175950
To: "gromacs.org_gmx-users@maillist.sys.kth.se"
Subject: [gmx-users] Use trjconv in parallel,
Hello,
in short : it is possible ? I use the gromacs v4.6.5.
Thanks
Stéphane
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buffer. The cluster pair list does have a buffering effect, but choosing
a larger rlist might be necessary for good energy conservation.
Stéphane
On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote:
> Dear GMX-users
>
> I have done a 90 ns long simulation of a heterogeneous
Dear GMX-users
I have done a 90 ns long simulation of a heterogeneous system (SPCE water,
phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with
GROMACS4.6.5. to compute related dynamical properties, I would like to continue
this simulation in NVE. But I am puzzled to c
Hello Rebeca,
Did you read my response to your (same) question in the AMBER mailing list? As
I said in this forum, I have developed parameters for AMBER for SDS. They can
be used with GROMACS (since I have the corresponding itp/top files). If you are
interested, please contact me directly.
S
Hello,
In addition with GridMat MD, you could use APL@Voro that reads the xtc
trajectory and plots the average area per lipid. The program uses the Voronoi
tesslation approach to compute the APL as it suggested by César Vila
http://www.aplvoro.org/
Good luck
--
OM line has thirty extra spaces and an X?
Mark
>
> Dr. Vitaly V. Chaban
>
>
> On Thu, Feb 20, 2014 at 12:47 PM, ABEL Stephane 175950
> wrote:
> > Hello all,
> >
> > My apologies for these out topic questions
> >
> > Does anybody have alrea
Hello all,
My apologies for these out topic questions
Does anybody have already try to convert xtc trajectory into xyz with
openbabel?
Btw, it seems that pdb file generated with editconf can not be read by
openbabel. I obtain the following error :
WARNING: Problems reading a PDB file
hello,
In our group, we have developed a tool called "trjVoronoi" that computes the
molecular volume (i.e. Voronoi Volume) and the associated surfaces) of the
whole cell and each molecular components from MD trajectories generated with
GROMACS or NAMD.
You can download it here:
https://sites
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