Dear Gromacs Specialists,
I am searched force field for Titanium (Ti) element. Parameters consist of
sigma and epsilon. Can you help me, Please?
Best Regards
Sara
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Dear Users,
I am running Protein-Ligand MD simulations. Whenever, i get to do the
Position restrain run of both my protein and ligand, i get this error;
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Protein in water'
5 steps,100.0 ps.
step 0
Step 8, time 0.016 (ps) LINCS
Thank you all for the reply, now I'm much less confuse and thank you
David for the paper.
I wanted to try implicit simulations because I need to speed up a bit my
simulations...but I think that now I'll try something else (coarse
grained/remd).
cheers
Fra
On Mon, 23 Sep 2013, at 08:28 PM,
OK seems it is my self-post, but incase anyone finds it, so they are not
mislead by the above.
After few more trial and fails, I think currently there is no tool to
assemble a periodic system from residues. So neither the approach with
specbonds, nor the periodic_molecule work for this case.
If it may be of help this paper
(http://www.ncbi.nlm.nih.gov/pubmed/?term=Systematic+Validation+of+Protein+Force+Fields+against+Experimental+Data)
compares several force field with experimental data.
It was useful to me at the time I read it.
cheers
Fra
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View this message in context:
I found this list useful:
http://md.chem.rug.nl/cgmartini/index.php/blog/265-comparingforcefields
http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2
On Wed, Sep 25, 2013 at 4:16 PM, fcarb frac...@myopera.com wrote:
If it may be of help this paper
(
On 9/25/13 4:54 AM, mohammad agha wrote:
Dear Gromacs Specialists,
I am searched force field for Titanium (Ti) element. Parameters consist of
sigma and epsilon. Can you help me, Please?
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
I sincerely doubt that a
On 9/25/13 6:05 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am running Protein-Ligand MD simulations. Whenever, i get to do the
Position restrain run of both my protein and ligand, i get this error;
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Protein in water'
5 steps,100.0
Dear Mark
The UNIX tool diff is your friend for comparing files.
Thanks for your suggestion. I used diff and sdiff toll
for comparing 2 files (before and after correction).
diff old.gro new.gro
These tolls did not give me any output file or text
containing difference between 2 files.
In this
Thank you very much from your answer.
Best Regards
Sara
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Wednesday, September 25, 2013 3:07 PM
Subject: Re: [gmx-users] force
Hi All,
I have a dopc+50% cholesterol bilayer. I want to selectively choose the
upper and lower leaflets. I used g_select the following way
g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol
and z6' (6 is the COM of my box)
I am getting the following error.
Possible bug:
Dear all,
I would like to calculate how three dihedrals in my
protein are evolving during the simulation time, but I don't understand
which is the correct command to do.
In particular, I would like to
know:
- what is the value of a specified dihedral (in degrees)
- if
this value changes
Hello,
On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.comwrote:
I have a dopc+50% cholesterol bilayer. I want to selectively choose the
upper and lower leaflets. I used g_select the following way
g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol
and
Thank you very much. My bilayers were initially built with packmol which is
probably why z6 worked. I will keep this in mind.
On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote:
Hello,
On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.com
wrote:
I
Basic question: How do I verify that the right atoms were chosen in the
index file? There are a lot of atoms.
On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan rajatdesi...@gmail.comwrote:
Thank you very much. My bilayers were initially built with packmol which
is probably why z6 worked. I will
On 9/25/13 12:24 PM, rajat desikan wrote:
Basic question: How do I verify that the right atoms were chosen in the
index file? There are a lot of atoms.
Pass the index file to trjconv and use it to parse out the atoms in the group
from the original coordinate file.
-Justin
On Wed, Sep
On 9/25/13 12:08 PM, Anna MARABOTTI wrote:
Dear all,
I would like to calculate how three dihedrals in my
protein are evolving during the simulation time, but I don't understand
which is the correct command to do.
In particular, I would like to
know:
- what is the value of a specified
If diff says there are no changes, then you're not comparing with the file
you changed...
On Sep 25, 2013 1:59 PM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear Mark
The UNIX tool diff is your friend for comparing files.
Thanks for your suggestion. I used diff and sdiff toll
for
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