Dear all,
I have a question regarding the g_sham which yields the free energy surface
from the two eigenvectors, now i would like to map the structures on to the
surface minima could any one tell me how to locate the structure with the local
minimas and a global minima
Thanks in advance
Rega
Hi Mark,
Thank you for your quick reply. So it seems that I have to do it on my own.
It's always good to ask - it's not productive to reinvent the wheel.
Best wishes,
Slawomir
Wiadomość napisana przez Mark Abraham w dniu 2011-07-19, o godz. 07:28:
> On 19/07/2011 12:16 PM, Sławomir Stac
Dear Gromacs Users,
As I know for the Energy Minimization algorithms both Steepest Descent and
Conjugate Gradient will not provide a global minimum of the potential energy
but only a local minium.
Does anyone know how Gromacs choose the starting point on the potential energy
hypersurface for th
On 19/07/11, "Marzinek, Jan" wrote:
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> As I know for the Energy Minimization algorithms both Steepest Descent and
> Conjugate Gradient will not provide a global minimum of the potential energy
> but only a local mi
Dear GROMCS users,
I am trying to convert some GLYCAM parameters in GROMACS format. For this
purpose, I am using the latest GLYCAM parameters downloaded from the RJ.
Woods’ website and the examples given in the acpype code (here for the
dihedral angles) :
http://code.google.com/p/acpype/source
Please keep gmx-users correspondence on the mailing list, so that others can
learn from and contribute to the discussion and/or archives.
On 19/07/11, "Marzinek, Jan" wrote:
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On 19/07/2011 11:56 PM, sa wrote:
Dear GROMCS users,
I am trying to convert some GLYCAM parameters in GROMACS format. For
this purpose, I am using the latest GLYCAM parameters downloaded from
the RJ. Woods' website and the examples given in the acpype code (here
for the dihedral angles) :
It is normal to have combinations of negative and positive values for the
barrier heights. Those are just the best coefficients to reproduce some QM
rotational energy curve during the parameterization. The negative
periodicities are a convention from AMBER. They simply indicate that the
dihedr
Hi all,
I am doing dppc-water simulation. I am using structure and topologies from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
In version 4.0 when i do
grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top
it creates npt.tpr without any errors.
Using the sam
Amit Choubey wrote:
Hi all,
I am doing dppc-water simulation. I am using structure and topologies from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
In version 4.0 when i do
grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top
it creates npt.tpr withou
Thanks Justin, I can see that there is no problem when i fix the
periodicity.
Amit
On Tue, Jul 19, 2011 at 2:52 PM, Justin A. Lemkul wrote:
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> Amit Choubey wrote:
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>> Hi all,
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>> I am doing dppc-water simulation. I am using structure and topologies from
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>> http://moose.bio.ucalgary.ca/
My simulation was performed within a triclinic box and I would like to
reshape it into a rectangular box for post-processing analysis. I tried
"/trjconv -o traj.pdb -ur rect -pbc -mol " but the new .pdb file still has
triclinic geometry. Can someone please help?
Thanks!
Max
--
gmx-users mailing
Dear gmx-users,
I am heating my system at 300 K.
I have set the pbc conditions as "no"
I get the following error:
---
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 5436
Fatal error:
pbc type no is not supported with domain
shivangi nangia wrote:
Dear gmx-users,
I am heating my system at 300 K.
I have set the pbc conditions as "no"
I get the following error:
---
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 5436
Fatal error:
pbc type no i
Hi,
I am trying to use inflategro to efficiently insert my protein into lipid
bilayer. I have been following the KALP-15 in DPPC tutorial to do so.
However, after running the perl script for the first time, I am not able
to perform energy minimisation. The error message that I get when I pre
proc
On 20/07/2011 12:28 PM, Sweta Iyer wrote:
Hi,
I am trying to use inflategro to efficiently insert my protein into lipid
bilayer. I have been following the KALP-15 in DPPC tutorial to do so.
However, after running the perl script for the first time, I am not able
to perform energy minimisation.
Sweta Iyer wrote:
Hi,
I am trying to use inflategro to efficiently insert my protein into lipid
bilayer. I have been following the KALP-15 in DPPC tutorial to do so.
However, after running the perl script for the first time, I am not able
to perform energy minimisation. The error message that
dear sir,
i was doing gromacs when i run pdb2gmmx i got following error that
is some atom missing
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hi dear users
is there any command in gromacs to determine mass center of a protein? I mean
to
find out witch atom or residue stands for mass center.
thanks,
sajad--
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