Hi
I am trying to simulate the self-assembly of course-grained DSPC lipids
into a lipid bilayer. I made a box (7.5 x 7.5 x 7.5) containing 128 DSPC
lipids, and added 768 molecules of water to the system, and ran a
minimization (using em.mdp). The summary of the results is below.
Reached the
On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
this atom is the CG atom of the phosphate I added to the protein.
But how can I find out by what it is punished?
Visualization.
This is the topology for this residue in the aminoacid.rtp file. I added
it
On 9/13/12 1:12 AM, James Starlight wrote:
Dear Gromacs Users!
I'm looking for possible way to resume trajectory calculations after
that calculations have been stoped.
Typically in such cases I start new task using cpt file from
incomplete run. This produce new trajectory which start from
Ah okey. Thank you.
I will write them.
Hmm, but the protein is a crystal structure from pdb with a resolution of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah okey. Thank you.
I will write them.
Hmm, but the protein is a crystal structure from pdb with a resolution of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md
Respected Sir / Madam
i did temperature study for that i
need analysis principal component analysis so, i followed GROMACS
Introductory Tutorial (4.5.5)
*g_covar*
g_covar -s md_0_2.tpr -f md_merged_20_ns.xtc -o 2KW8_275_eigenval.xvg -v
2KW8_275_eigenvect.trr
Justin,
I've used
grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o
incomplete.tpr
mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append
where incomplete.cpt was checkpoint from previous run and -o
incomplete.tpr was the name for new trajectory (in that case its equal
On 9/13/12 9:56 AM, James Starlight wrote:
Justin,
I've used
grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o
incomplete.tpr
mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append
where incomplete.cpt was checkpoint from previous run and -o
incomplete.tpr was the
Dear All,
Could you please write me which is the latest version of Charmm force
field for proteins? I want to study protein folding in explicit
solvent. Is it available in Gromacs?
Steven
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
*
charmm27 is the canonical charmm protein FF, which is supported by gromacs.
Note that if you are using gromacs prior to 4.5.5 to use -nochargegrp when
using pdb2gmx when parameterizing your protein.
On 2012-09-13 04:19:16PM +0100, Steven Neumann wrote:
Dear All,
Could you please write me
Dear Justin Thank you for your Previous reply,
sorry for the inconvenience to you personal Mail.
I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation in
pdb file are ignored . so that it is not
On 9/13/12 11:42 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply,
sorry for the inconvenience to you personal Mail.
I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation
Thought people might want to know that thanks to the XTC Library, Chimera now
support reading trajectories where the coordinates are in .xtc format. That
support is only in the daily build of Chimera, not the production release.
www.cgl.ucsf.edu/chimera
--Eric
Eric
#
CALL FOR PAPERS
3rd International Workshop on
Model-driven Approaches for Simulation Engineering
part of the Symposium on Theory of Modeling and Simulation
(SCS
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with
some polymers. and I have some problems in forming the topology files. I have
actually two questions and I hope you can help me in that.
(1) In an attempt to form the topology files of CNTs and graphene (using
x2top),
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