Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So, the the LJ energy is coming as zero. But the coulomb potential is
non zero. What should I do to make it zero?
Energies (kJ/mol)
GB PolarizationLJ (SR) Coulomb (SR) Potential
On 18/08/12, *jesmin jahan * shraba...@gmail.com wrote:
Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So, the the LJ energy is coming as zero. But the coulomb potential is
non zero. What should I do to make it zero?
Each charge-charge
Okay thanks. I got it. :-)
Best Regards,
Jesmin
On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 18/08/12, *jesmin jahan * shraba...@gmail.com wrote:
Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So,
Hi Mark,
Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:
Energies (kJ/mol)
Bond AngleProper Dih. Improper Dih.GB Polarization
1.54109e+043.84351e+038.47152e+03
On 16/08/2012 4:26 PM, jesmin jahan wrote:
Hi Mark,
Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:
Energies (kJ/mol)
Bond AngleProper Dih. Improper Dih.GB Polarization
Hi Mark,
Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the the bonded terms and zero the VDW parameters?
I really need to compare how fast different well known package can
compute GB-polarization energy and how good the energy
On 16/08/2012 5:08 PM, jesmin jahan wrote:
Hi Mark,
Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the the bonded terms and zero the VDW parameters?
In the .top file from which you made the .tpr. (And contributing .itp
files)
Hi Mark,
According to your advice remove the the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
], and run the simulation mdrun rerun.
I got output something like the following:
Energies (kJ/mol)
GB PolarizationLJ
On 17/08/2012 1:14 PM, jesmin jahan wrote:
Hi Mark,
According to your advice remove the the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
],
This only removes the bonded terms (in the sense of those atoms that
interact
Thanks Mark for your reply. I was trying to use Single-Point Energy
Calculation as you advised in your first reply but for most of the
files the simulation failed because I was using the original .pdb
files in the mdrun command.
Anyways. I really appreciate your help.
Thanks again,
Jesmin
On
On 14/08/2012 7:38 AM, jesmin jahan wrote:
Dear Gromacs Users,
I have some questions regarding GB-Polarization Energy Calculation
with Gromacs. I will be grateful if someone can help me with the
answers.
I am trying to calculate GB-Polarization energy for different Protein
molecules. I am
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