Elisabeth wrote:
Hello to all,
I am looking for bonded and nonbonded parameters for C H atoms in
saturated hydrocarbons.
atom types are:
Carbon atoms opls_135 opls_136
H opls_140
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
opls_1401.00800 ; a
Dear gromacs users
in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor -
Donor - Hydrogen)
-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)]
I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A.
and angle of 30 = acceptor-donor–hydrogen an
Deer users
The simulation box contains sodium and chloride ions
start simulation
pdb2gmx -f ion.pdb -posrefc 0
Force Field : AMBER99SB-ILDN - Water TIP3P
editconf -f conf.gro -bt cubic -box 3 3 3
genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top
grompp -f minim.mdp -c 5.gro -p topo
Dear users
The simulation box contains sodium and chloride ions
start simulation
pdb2gmx -f ion.pdb -posrefc 0
Force Field : AMBER99SB-ILDN - Water TIP3P
editconf -f conf.gro -bt cubic -box 3 3 3
genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top
grompp -f minim.mdp -c 5.gro -p topol
atila petrosian wrote:
Dear gromacs users
in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor
- Donor - Hydrogen)
-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)]
I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A.
and angle of 30
Saeid Akbarshahi wrote:
Deer users
The simulation box contains sodium and chloride ions
start simulation
pdb2gmx -f ion.pdb -posrefc 0
Force Field : AMBER99SB-ILDN - Water TIP3P
editconf -f conf.gro -bt cubic -box 3 3 3
genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top
grompp -f
Thanks very much.
I am sorry I did not describe my question very clear. In my system, I am going
to obtain three things. (1) the free energy versus distance, which I can obtain
from g_wham. (2) the free energy versus, eg, the radius of gyration of the
object A. (3) the 2-D free energy as a func
Hi,
I was planning to use Thermodynamic integration to calculate solvation free
energy of a molecule in a solvent. I was following Justin Lemkul's online
tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
. I found that
a) a sd int
Sanku M wrote:
Hi,
I was planning to use Thermodynamic integration to calculate solvation
free energy of a molecule in a solvent. I was following Justin Lemkul's
online tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
. I found t
Hi,
I used the inflategro.pl script to insert my protein into the membrane and
scaled down the lipids until it reached the recommended area per lipid
value. After removing 4 lipid molecules, I started with an area of 90
square angstrom and reached a value of 65 square angstrom within just 5
iterat
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Thursday, August 4, 2011.
For all questions about CloudBroker and the CloudBroker Platfo
Sweta Iyer wrote:
Hi,
I used the inflategro.pl script to insert my protein into the membrane and
scaled down the lipids until it reached the recommended area per lipid
value. After removing 4 lipid molecules, I started with an area of 90
square angstrom and reached a value of 65 square angstro
Please keep the discussion on the list; I'm not a private tutor.
Saeid Akbarshahi wrote:
Dear Justin
I have simulated this system with this structure and files.Could you
tell me, is my structure correct?
I have no clue what is in your system, what settings were used for the
simulation, o
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