Hi,
This is my input file for calculating bilayer thickness in absence of peptide:
## Input file and input file parameters
coord_file md.gro
file_type gro
num_frames 1
num_lipid_types1
resname1POPC
atomname1 P8
sol
Dear Gromacs users,
I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few
analysis. Unfortunately I ended-up with the following error.
GROMACS will now assume it to be a trajectory and will try to open it using
the
Hi,
Have look here:
http://haddock.science.uu.nl/services/HADDOCK/library.html
The ff used by HADDOCK is oplsx derived from opls. Maybe you can exploit them
as starting point.
Hope it helps
And
"Martin, Erik W" ha scritto:
I've searched the literature and internet and can't seem to find an
I've searched the literature and internet and can't seem to find anything. I
need to rerun some simulations I've run previously with OPLS-AA (and eventually
gromos 54A7 when I'm done with OPLS) and need to include phosphorylated
residues. I'm parameterized residues in Amber and Charmm, so I'm
On 10/17/13 2:09 PM, Shima Arasteh wrote:
I used -fit or boxcenter or trans or .. any other thing which I though to solve
my problem, but did not work. Would you give me a hint pleaaasssee?
trjconv -center
or
trjconv -fit transxy
-Justin
--
==
I used -fit or boxcenter or trans or .. any other thing which I though to solve
my problem, but did not work. Would you give me a hint pleaaasssee?
Thanks a lot.
Sincerely,
Shima
On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul wrote:
On 10/16/13 8:29 AM, Shima Arasteh wrote:
>
>
On 10/14/13 7:47 AM, Sathya wrote:
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
I have few questions. Please help me to solve it.
1) After the topol.top file has genera
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
I have few questions. Please help me to solve it.
1) After the topol.top file has generated from pdb2gmx is it necessary to
add
On 10/17/13 1:01 PM, sunyeping wrote:
Dear Gromacs users,
I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro
-p topol.top -pname NA -nname CL -np 8
but it returns a error message saying:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section
Dear Gromacs users,
I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro
-p topol.top -pname NA -nname CL -np 8
but it returns a error message saying:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'
I checked the topol.
Hi Chris,
I mentioned that PS would have helped! I am sorry about the confusion. I should
have been more clear. I guess you have not followed the particle decomposition
threads lately :))
The PD option has been associated some serious issues lately … notably I
noticed it does not work well i
This is my own experience, someone may have better suggestions. First, you can look on the internet for .py .c++ or java matix manupulation tools/small programs run in bash shells. These allow the output from the g:sham or other (2d or 3d) to be turned into mtricies. These can then be fed into
Thanks for the hint XAvier.
Unfortunately, I get crashes with particle decomposition (see below). If I use
either DD or PD, I can run on up to 2 threads
without adjusting -rdd or -dds. I can only use >2 thread with DD if I set -rdd
2.8. If I try to use more than 2 threads with PD,
I get lincs
Yes it is a pity!
But particle decomposition helps :)) well helped!
>
> It's a shame that long distance restraints limit the parallalization so much,
> but it is understandable. Thanks for helping me with this.
>
> Chris.
>
> -- original message --
>
> Initializing Domain Decomposition on
Indeed, sorry that I didn't notice that, Mark. Looks as if the two-body bonded
interaction gets multiplied by 1.1/0.8 so I suppose that this is working as it
should.
It's a shame that long distance restraints limit the parallalization so much,
but it is understandable. Thanks for helping me wit
Hi,
On Oct 17, 2013, at 2:25 PM, pratibha kapoor wrote:
> Dear gromacs users
>
> I would like to run my simulations on all nodes(8) with full utilisation of
> all cores(2 each). I have compiled gromacs version 4.6.3 using both thread
> mpi and open mpi. I am using following command:
> mpirun -n
Dear gromacs users
I would like to run my simulations on all nodes(8) with full utilisation of
all cores(2 each). I have compiled gromacs version 4.6.3 using both thread
mpi and open mpi. I am using following command:
mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro
But I am getting following
On 10/16/13 10:32 PM, Sathya wrote:
Dear Justin,
I am currently working on Dynamics study of DPPC lipid bilayer and
chromium ions..
I want to know how to insert chromium ions into lipid bilayer. Is
there any software for this?
Please suggest some idea about how to inser
On 10/17/13 4:57 AM, Archana Sonawani-Jagtap wrote:
Hi,
I want to plot
1. -SCD (lipid tail order parameters) profile for both the chains (sn1 and
sn2)
2. Lateral diffusion of lipids
3. density profiles
in presence and absence of peptide.
I have plotted the above parameters in presence o
Hi,
Please tell me what is wrong in my input file. I am not getting APL
along with std deviation values.
Following is the input and output for calculating APL
Input file
coord_file md.gro
file_type gro
num_frames1
num_lipid_types 1
resname1
Try cgmartini.nl
On Oct 16, 2013, at 10:29 PM, 朱文鹏 wrote:
> Dear GMX users,
>
> I am going to do some coarse-grained simulations in which the lipid
> bilayeris covered by
> polysarccharide. I remember the website of Martini Force Field (http://md
> .chem.rug.nl/cgmartini/) provides a database
A postdoctoral position in simulations of membranes and membrane proteins
is available from 1 December 2013 (starting date flexible) for one year
(with possible extension) at the University of Southern Denmark (SDU),
Odense in the group of Dr Himanshu Khandelia.
Knowledge of statistical physics i
Hi,
I want to plot
1. -SCD (lipid tail order parameters) profile for both the chains (sn1 and
sn2)
2. Lateral diffusion of lipids
3. density profiles
in presence and absence of peptide.
I have plotted the above parameters in presence of peptide, for calculating
in absence of peptide, do i ne
4.5 can only handle about 500-1000 atoms per processor. Details vary.
Mark
On Oct 17, 2013 5:39 AM, "Nilesh Dhumal" wrote:
> Thanks for you reply.
>
> I am doing simulation for ionic liquids BMIM + CL. Total number of atoms
> are 3328.
>
> Nilesh
>
> > Assuming you're using LINCS, from the manua
Hi,
The log file gives a breakdown of how the minimum cell size was computed.
What does it say?
Mark
On Oct 17, 2013 5:17 AM, "Christopher Neale"
wrote:
> I have a system that also uses a set of distance restraints
>
> The box size is:
>7.12792 7.12792 10.25212
>
> When running mdrun -nt
Hi,
I'm trying to calculate the free energy of solvation of a relatively
large polymer molecule (161 atoms). I went through the free energy
tutorial published on J. Lemkul's web page but when trying to apply
the same approach to my case, the simulations typically fail. The
files for one such case
You do need a C compiler, not a Fortran one, and IIRC gcc 4.6.2 has some
known issues. Please follow the instructions in the install guide and get
the latest compiler you can.
Mark
On Oct 17, 2013 8:30 AM, "张海平" <21620101152...@stu.xmu.edu.cn> wrote:
> Dear professor:
> When I install the Groma
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