There was a tutorial on implementing a z-dependent electric potential
on the gromacs web page not that long ago. It didn't seem that
difficult. That should serve as a good starting point for your wall
o' carbon.
/Erik
27 jul 2007 kl. 01.56 skrev Mark Abraham:
Dear gmx users,
my apologies
27 jul 2007 kl. 09.53 skrev Erik Marklund:
There was a tutorial on implementing a z-dependent electric
potential on the gromacs web page not that long ago. It didn't seem
that difficult. That should serve as a good starting point for your
wall o' carbon.
...namely http://wiki.gromacs.o
On 7/27/2007 4:53 AM, Christopher Stiles wrote:
Ok here is the update:
I have made the following changes:
I almost doubled my box size and limited the saturation to 256 water
molecules.
I removed the include from my *.mdp file
Changed the includes in my topology file to:
#include "ffgmx.itp"
#inc
Dear GROMACS Community,
I'm having problem adding spc water molecules into my system containing lipids
molecules totaling 64 of them. My simulation box size is 1000 nm^3. I told
genbox to fill the simulation box with 100 nm^3 of spc216 water molecules using
option (-box 4.642 4.642 4.642) due
They are in the ffgmx.itp file and maybe I missed it but I didn't read about
people having to change it for CNT's, but maybe so I will look further into
this and try some things... I will let you guys know where I get. Also if
any one knows already knows please feel free to give me a hint or ref.
Dhananjay,
Consider searching the list archive... All possible solutions are in there.
Cheers,
Tsjerk
On 7/27/07, Dhananjay <[EMAIL PROTECTED]> wrote:
> Hello all,
>
> I am getting error in pr dynamics when I run mdrun for a protein consist of
> two chains with 326 residues each.
>
> The error
Lee-Ping,
Just a friendly reminder when responding or posting make sure you
change the subject of you're your response to something appropriate just as
it says to do in the beginning of each digest.
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE) State University of
The warnings are:
...
WARNING 701 [file "SWNT_6_6_144.top", line 1278]:
No default Angle types, using zeroes
WARNING 702 [file "SWNT_6_6_144.top", line 1278]:
No default Angle types for perturbed atoms, using normal values
...
WARNING 793 [file "SWNT_6_6_144.top", line 1327]:
No default Prope
hi,
did u specify an index file in your command line for the 2 groups (protein
and SOl?
> Dhananjay,
>
> Consider searching the list archive... All possible solutions are in
> there.
>
> Cheers,
>
> Tsjerk
>
> On 7/27/07, Dhananjay <[EMAIL PROTECTED]> wrote:
>> Hello all,
>>
>> I am getting e
Hi all.
Well, I just tried something different, and it "worked".
Found on the net that the 3.3.1 version of gromacs allows me to use sum of
different periodic potential for the same dihedral, making it unecessary to
use RBs. So, if I write the dihedrals in the form:
F CTCTF 1
Did you define angle and dihedral parameters in the [ angletypes ] and
[ dihedraltypes ] sections of your .itp file?
Bob
On 7/27/07, Christopher Stiles <[EMAIL PROTECTED]> wrote:
> The warnings are:
> ...
> WARNING 701 [file "SWNT_6_6_144.top", line 1278]:
> No default Angle types, using zeroes
Thank you Lars, and everybody who volunteered their help.
I've been using "make mdrun" in building my modified Gromacs and it works
great in Linux. Under Windows, I'm still running into a problem where it
tells me "mdrun is up to date". It's not a big deal though, since it builds
so much faster
Lars Schaefer wrote:
Lee-Ping wrote:
Hi there,
I'm editing the bondfree.c source code in gromacs. The problem is,
every
time I launch mdrun to see what my program does, it recompiles not only
bondfree.c, but every single tool in the src/tools directory! It
seems like
an unnecessary was
27 jul 2007 kl. 10.44 skrev Alif M Latif:
Dear GROMACS Community,
I'm having problem adding spc water molecules into my system
containing lipids molecules totaling 64 of them. My simulation box
size is 1000 nm^3. I told genbox to fill the simulation box with
100 nm^3 of spc216 water mole
Hello all,
I am getting error in pr dynamics when I run mdrun for a protein consist of
two chains with 326 residues each.
The error is as follows:
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131
Fatal error:
Not enough ref_t and tau_t values!
-
Hello users,
I am trying to check wether my prepared system is ready to
be put into a simualtion. I have a 2 body system 1protein +
1peptide. I have prepared the peptide using PRODRG server
and included it into the protein .top file. I wanted to do a
dummy minimization run with my prepared prote
On one hand, use -pp for grompp for whatever warnings, so you may what's
on the line which causes problems.
On the other hand, find force field parameters for carbon nanotubes. For
a simple rigid nanotube, I reckon that you may only need bond potential
for every bond.
On 7/27/2007 10:42 PM, Ch
Thank you David, I really appreciated your help. I will read your paper and
try to go on.
Thank you very much!
2007/7/27, David Mobley <[EMAIL PROTECTED]>:
>
> Hi,
>
> > I am trying to run some simulations in attempts to calculate binding
> free
> > energy between ligands and a protein using the F
Hi all,
I am in need of simulating C500 molecules in bulk.
1 Particles is a good number for me for testing some order parameter codes.
Does anyone have relevant .gro, .itp, .mdp, .top files for the same ? It will
be a great help.
~ Rohit
___
You could probably dispense with the dihedral terms (as long as you
aren't interested in the mechanical properties of the CNT), but I
would at least include a bond and angle term for the nanotube atoms.
On 7/27/07, Yang Ye <[EMAIL PROTECTED]> wrote:
> On one hand, use -pp for grompp for whatever
Hi all.
Well, I'm having a few problems in implementing an opls-like dihedral
potential, what mean, a serie of different periodic dihedral potentials.
After much problem with the RB potential conversion, Ifound on the net that
the 3.3.1 version of gromacs allows me to use sum of different periodi
ROHIT MALSHE wrote:
Hi all,
I am in need of simulating C500 molecules in bulk.
1 Particles is a good number for me for testing some order parameter codes.
Does anyone have relevant .gro, .itp, .mdp, .top files for the same ? It will be a great help.
I'll offer you long odds against an
pkmukher wrote:
Hello users,
I am trying to check wether my prepared system is ready to
be put into a simualtion. I have a 2 body system 1protein +
1peptide. I have prepared the peptide using PRODRG server
and included it into the protein .top file. I wanted to do a
dummy minimization run with
[EMAIL PROTECTED] wrote:
hi,
did u specify an index file in your command line for the 2 groups (protein
and SOl?
If you don't specify an index file, GROMACS will define such groups by
default. I'm guessing the problem is arising because there's something
else in the system that you need to i
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