Hi everyone. I ran an umbrella sampling simulation of a protein in a
membrane. I used pull_geometry=cylinder. I tried to analyze the results with
g_wham. I got this error:
Fatal error:
With pull geometry 'cylinder', expected pulling in Z direction only.
However, found dimensions [Y Y Y]
The manu
On 11/02/2012 9:54 AM, Tom wrote:
Dear Gromacs Users
I am confused about definition of improper dihedral angle in charmm27,
which is compared to oplsaa.
Why charmm ff in gromacs give *double* items for the same dihedral angle.
e.g. for charmm27 ASN
CG ND2 CB OD1
CG C
On 11/02/2012 4:15 AM, francesca vitalini wrote:
Ok now I have tryied to restart it all and the problem seems to be
that the system has some overlapping. In fact, no matter what I
freeze, water, CA or nothing, I get this error message
VERSION 3.3.1
This program is free software; you
On 11/02/2012 2:48 AM, francesca vitalini wrote:
In fact in the reverse transformation I'm feeding the CG structure
information.
Yes, but you need a source of atomistic intra-residue knowledge about
protein structure in order to convert a CG structure to something that
is vaguely plausible at
Dear Gromacs Users
I am confused about definition of improper dihedral angle in charmm27,
which is compared to oplsaa.
Why charmm ff in gromacs give *double* items for the same dihedral angle.
e.g. for charmm27 ASN
CG ND2 CB OD1
CG CB ND2 OD1
N
On Fri, Feb 10, 2012 at 4:11 PM, David van der Spoel
wrote:
>
> Op 10 feb 2012 om 22:55 heeft Abhijeet Joshi het
> volgende geschreven:
>
> Hi ,
> I am also working on similar systems. Can you tell me where and
> what LJ parameters you specified for halides
>
>
> You need the anharmonic t
Op 10 feb 2012 om 22:55 heeft Abhijeet Joshi het
volgende geschreven:
> Hi ,
> I am also working on similar systems. Can you tell me where and what
> LJ parameters you specified for halides
You need the anharmonic term for polarisation. It is implemented in the
development version o
Hi ,
I am also working on similar systems. Can you tell me where and
what LJ parameters you specified for halides
Thanks in advance,
Abhijeet
On Fri, Aug 12, 2011 at 8:56 AM, zhongjin wrote:
> Dear GMX users,
>I am using GMX4.5.4 to simulate SWM4-NDP polarizable water model,
> i
Ok now I have tryied to restart it all and the problem seems to be that the
system has some overlapping. In fact, no matter what I freeze, water, CA or
nothing, I get this error message
VERSION 3.3.1
This program is free software; you can redistribute it and/or
modify it under
Hi,
i second Justins seond idea (creating a small box of equilibrated CCl4
and then fill the simulation box via the -cs option).
Depending if you have other molecules in your system, make the
simulation box a little bit bigger, because you will get some holes. In
the subsequent NPT simulation t
In fact in the reverse transformation I'm feeding the CG structure
information.
Once I look through VMD to the FG structure I notice that the backbones are
not in planes so definitely I need to run some minimization there. In the
tutorial they were using simulating annealing, but I don't think I ne
On 2012-02-10 16:14, Jon Kapla wrote:
Dear users,
I'm trying out the relatively new phospholipid parameters from Poger et.
al. 2010 (DOI: 10.1002/jcc.21396), by simulating a box of a DMPC bilayer
and approx. 30 SPC water molecules per lipid. I'm getting very low
lateral diffusion compared to bot
Dear users,
I'm trying out the relatively new phospholipid parameters from Poger et.
al. 2010 (DOI: 10.1002/jcc.21396), by simulating a box of a DMPC bilayer
and approx. 30 SPC water molecules per lipid. I'm getting very low
lateral diffusion compared to both other force fields (like Berger) a
I know what is happening... I am tired :)
I used previous pdb file before moving my complex and just realised after
fighting so long, sorry for my message.
Have a good weekend,
Steven
On Fri, Feb 10, 2012 at 2:54 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I am preparing my protein-ligand c
Dear Gmx Users,
I am preparing my protein-ligand complex system for Umbrella Sampling (free
binding energy of ligand) and I set
up the box (Pulling with Z coordinate):
editconf -f Protein10LIGrot.pdb -o ProteinLIGbox.pdb -box 12 7 13
Then using VMD I placed my Protein-Lig complex to on the r
On 11/02/2012 1:19 AM, Elisabeth wrote:
Hello all,
Does the shift function use group based truncation?
See the discussion of charge groups in manual section 3.4.2.
Thanks Mark.
-1- First of all if I am right charge groups in gromacs language in
identical to "group based trun
> Hello all,
>
> Does the shift function use group based truncation?
>
>
> See the discussion of charge groups in manual section 3.4.2.
>
Thanks Mark.
-1- First of all if I am right charge groups in gromacs language in
identical to "group based truncations"?
Manual 342: "This reduces the cut-o
Hi Elisabeth,
You could check the following paper:
D. van der Spoel and P. J. van Maaren. The origin of layer structure
artifacts in simulations of liquid water. J. Chem. Theory Comput.,
2:1, 2006.
Aldi
On Fri, Feb 10, 2012 at 4:58 PM, Mark Abraham wrote:
> On 11/02/2012 12:52 AM, Elisabeth wro
On 11/02/2012 12:52 AM, Elisabeth wrote:
Hello all,
Does the shift function use group based truncation?
See the discussion of charge groups in manual section 3.4.2.
In the manual I see: by using shifted forces there is no need for
charge groups (=group based?!) in the neighbor list?
Can an
On 11/02/2012 12:41 AM, francesca vitalini wrote:
In order to overcome the problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want the structure to be
maintained). However, if I do then I have problems with the energy
minimization as the force on the 15300 is
Hello all,
Does the shift function use group based truncation? In the manual I see: by
using shifted forces there is no need for charge groups (=group based?!) in
the neighbor list?
Can anyone shed some light on calculation of shifted forces?
Thanks,
Eli
--
gmx-users mailing listgmx-users@g
In order to overcome the problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want the structure to be
maintained). However, if I do then I have problems with the energy
minimization as the force on the 15300 is infinite.
Getting Loaded...
Reading file EM1-1.tpr,
James Starlight wrote:
Justin,
2012/2/6 Justin A. Lemkul mailto:jalem...@vt.edu>>
Some simple calculations using the desired density and the box
dimensions (to get the volume) will tell you exactly how many
molecules you need. If you only "suppose" you've got a reasonable
n
francesca vitalini wrote:
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520(parto of the
protein)
Norm of force = 2.2836
Dear Kiwoong Kim,
you will find your answer here:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
Best
Kathleen
--
Kathleen Kirchner
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Le
Thanks to Azoia and nayeem
The solution from Azoia is perfectly working :)
Thx.
2012/2/10 Nuno Azoia
> There is a more direct way. In the script just use
> g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm < Number
> Number
> EOF
>
> where Number denotes the group number, or the group name, matchin
There is a more direct way. In the script just use
g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm < wrote:
> Create a file named input.g_rms. write the group number in this file. In
> your shell script after command line write executed in shell the file input.g_rms having group number will be read.
>
Create a file named input.g_rms. write the group number in this file. In
your shell script after command line write wrote:
> Hi,
>
> I'm not good at shell programming now.
> For the simplicity, I wrote down all the gromacs commands in one shell
> script.
>
> It means that if I execute the .sh fil
Justin,
2012/2/6 Justin A. Lemkul
>
> Some simple calculations using the desired density and the box dimensions
> (to get the volume) will tell you exactly how many molecules you need. If
> you only "suppose" you've got a reasonable number, there are better ways to
> be sure ;)
>
>
In accordan
Hi,
I'm not good at shell programming now.
For the simplicity, I wrote down all the gromacs commands in one shell
script.
It means that if I execute the .sh file, then every works including graphs
used for analysis are done.
However, when there are g_msd -f *.xtc -s *.tpr -o *.xvg -rmcomm, I have
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520(parto of the
protein)
Norm of force = 2.28369808518165e+06
and the system l
On 2012-02-10 10:35, Tsjerk Wassenaar wrote:
Well, I don't think excel will be a convenient tool for this. Why not
try awk for a change?
paste msd*.xvg | awk '/^[^@#&;]/{S=0;N=0; for (i=2;i<21; i+=2)
{S+=$i;N++}; print S/N}'
Otherwise a few lines of python would also do the trick.
Cheers,
Tsj
Well, I don't think excel will be a convenient tool for this. Why not
try awk for a change?
paste msd*.xvg | awk '/^[^@#&;]/{S=0;N=0; for (i=2;i<21; i+=2)
{S+=$i;N++}; print S/N}'
Otherwise a few lines of python would also do the trick.
Cheers,
Tsjerk
On Thu, Feb 9, 2012 at 1:56 PM, lina wrot
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