On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy nancy5vi...@gmail.com
wrote:
In an earlier message, it was stated that topolbuild generated
topologies with Gromos 53a6
and OPLS-AA force fields. I am using
topolbuild (version 1.2.2), and the only files in the
dat/gromacs
directory are for
I'm glad to be of help; yes, I would like to beta test topolbuild 1.3.
Thank you.
On Thu, Aug 13, 2009 at 7:42 AM, Bruce D. Ray bruced...@yahoo.com wrote:
On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy nancy5vi...@gmail.com
wrote:
In an earlier message, it was stated that topolbuild
Hello,
In an earlier message, it was stated that topolbuild generated topologies
with Gromos 53a6 and OPLS-AA force fields. I am using topolbuild (version
1.2.2), and the only files in the dat/gromacs directory are for the force
fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. How is the OPLS-AA
Thank you for the article.
Nancy
On Mon, Aug 10, 2009 at 9:34 PM, Dallas B. Warren
dallas.war...@pharm.monash.edu.au wrote:
You might want to consider the parameters I developed for propylene
glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms
The structure in the original PDB file of ethylene glycol was in the gauche
conformation. When I minimised the solvated system, the molecule remained
in the gauche conformation. However, during equilibration of the system,
the conformation of the molecule changed to trans within less than one
On Sunday, August 9, 2009 at 4:32:19 PM, Nancy nancy5vi...@gmail.com wrote:
I obtained the ethylene glycol (1,2-ethanediol) structure from the URL:
http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb
I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF
Chimera
You might want to consider the parameters I developed for propylene
glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms of the parameterisation of ethylene glycol.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and
Message-
From: gmx-users-boun...@gromacs.org on behalf of Nancy
Sent: Sat 8/8/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors
Hello,
I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed
: Sat 8/8/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors
Hello,
I have successfully minimised and equilibrated ethylene glycol in a
water
box. I have noticed that there seem to be no hydrogen bonds between the
solute
Hello,
I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules. Is this a normal behavior during minimsation
Nancy wrote:
Hello,
I have successfully minimised and equilibrated ethylene glycol in a
water box. I have noticed that there seem to be no hydrogen bonds
between the solute and solvent, but there are hydrogen bonds forming and
breaking between solvent molecules. Is this a normal behavior
While minimising ethylene glycol, I have no defines, and constraints are set
to none. During equilibration, define is set to -DFLEXIBLE, and constraints
are set to all-angles. Which parameters would affect hydrogen bonding?
I have one glycerol molecule in the center of a box of 609 water
Nancy wrote:
While minimising ethylene glycol, I have no defines, and constraints are
set to none. During equilibration, define is set to -DFLEXIBLE, and
constraints are set to all-angles. Which parameters would affect
hydrogen bonding?
Try constraints = all-bonds. You should not use
Hello,
I have successfully minimised and equilibrated one glycerol molecule in a
box of water (using the .mdp files below).
I noticed that during both minimisation and equilibration, solvent molecules
(waters) form many more hydrogen bonds between each other than the solute
(glycerol) forms to
Nancy wrote:
Hello,
I have successfully minimised and equilibrated one glycerol molecule in
a box of water (using the .mdp files below).
I noticed that during both minimisation and equilibration, solvent
molecules (waters) form many more hydrogen bonds between each other than
the solute
/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors
Hello,
I have successfully minimised and equilibrated ethylene glycol in a water
box. I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen
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