Hi all,
I want to modify the vdw radii of some atoms, but I did not find the file
that I can edit for this purpose. I checked the file vdwradii.dat, but I
did not find the atoms that I want to modify. Could someone tell me where I
can modify them? Thanks very much!
All the best,
--
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Dear GMX users,
There is a copper ion with four ligands in my system. I am going to
study this system using MD simulations.
For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from
one paper will be used in our
simulations. I already found the parameters of copper ion (Cu2+) in
Dear Dr. Vitaly Chaban,
Thanks very much for your reply. My question is the relationship between
van der Waals radius and sigma in the OPLS-AA/L force filed files of
Gromacs.
Of course I did ab initio optimizations of my system, but I do not know
there is some relation between the optimal
at 10:36 AM, fantasticqhl fantastic...@gmail.com
mailto:fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your reply. My question is the relationship
between van der Waals radius and sigma in the OPLS-AA/L force
filed files of Gromacs.
Of course I did ab
copper-ligand interactions using Coulomb+LJ
potential only? I would guess it is a chemical bonding case. Maybe the
Morse potential (additionally) can be of better service?
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.com
mailto:fantastic...@gmail.com wrote
potentials (Coulombic attraction in case of
OPLS).
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl fantastic...@gmail.com
mailto:fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for concern on my research! We are going to the
use the bonded
. Vitaly Chaban wrote:
On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.com
mailto:fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your patient explanation. Yeah, you are
right, that is what I want to know: how you tuned this parameter
and suggestions on this problems!
All the best,
Qinghua Liao
On 04/09/2013 10:03 AM, Dr. Vitaly Chaban wrote:
On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.com
mailto:fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your patient and detailed
Dear Dr. Vitaly Chaban,
Thanks very much for your explanation. I will try to use the method as
you suggested to do the validation. Thanks!
All the best,
Qinghua Liao
On 04/09/2013 12:10 PM, Dr. Vitaly Chaban wrote:
On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl fantastic...@gmail.com
Dear GMX users,
Just a simple question, are the Coulomb interactions calculated using
charges from ffnonbonded.itp or aminoacid.rtp?
Normally, they are the same. However, if I modify some charges for some
atoms (for example CB) of some residues in the aminoacid.rtp,
but do not modify in
Dear all,
But I have questions about the energies calculated by GMX for bonds and
angles scanning.
For example, a series of conformations of one system should be generated for
a bond scanning, the only difference in geometry of these conformations is
the bond length A---B.
However, when I set
Thank you, all! I know the reason now!
All the best,
qh
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Dear All,
I want to do the single point calculations for my systems with gromacs, I
used the method mentioned on the gmx's website.
mdrun -s sp.tpr -rerun configuration.pdb.
However, I have some questions on how to generate the tpr file for single
point calculation. It didn't work if I used a
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol
Dear Justin,
I am sorry for the late reply. I still can't figure it out.
Could you please send me the mdp file which was used for your single point
calculations.
I want to do some comparison and then solve the problem.
Thanks very much!
All the best,
Qinghua
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reasonable than those from single point calculation with rerun.
Do you know the possible reasons which could result in the huge
difference? Or I made some mistake?
Thanks very much!
All the best,
Qinghua
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com wrote:
Dear Justin
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