On 1/10/19 2:17 AM, Mark Abraham wrote:
Hi,
That's the wrong way around. :-) One doesn't do a lab experiment first and
then decide what you wanted to observe from it, to either :-). There are
tutorials for computing free energy of solvation, which I suggest you
follow, and I suspect your full
Hi,
That's the wrong way around. :-) One doesn't do a lab experiment first and
then decide what you wanted to observe from it, to either :-). There are
tutorials for computing free energy of solvation, which I suggest you
follow, and I suspect your fully solvated simulation won't be useful for
tha
Dear all users,
I am new for using GROMACS. and also read the tutorial of Methane and water. I
have already simulated data of 100 ns for four histones. I want to know how to
calculate free energy solvation from this data. which topology file and
coordinate files I will use?
I will appreciate you
Hello Tasneem,
Same like you, I'm pretty new to this field too. I don't know enough how to
calculate free energy in gromacs. I did only MM/PBSA for binding energy
calculations.
I'll let you know if i get some thing relevant to your question.
All the best.
Thanks
On Thu, Jan 5, 2017 at 10:28 PM,
Thanks again
That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.
W
well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations
good luck
On Jan 7, 2017 2:01 PM, "t
Thanks Amir Zeb for your reply
I have read in literature about the FEPsetup to parametrize the complex
file (protein+drug) for simulation. This setup builds files based on amber.
Since I have previously used 54a7ff to simulate the protein and drug and
topology files were generated from ATB in gromo
alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?
On Jan 7, 2017 1:38 PM, "tasneem kausar" wrote:
> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 A
mm/pbsa calculates binding energy. I have used that.
On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb wrote:
> hello
> you may use mm/pbsa compiled with gromacs to calculate free energy
> all the best
>
> On Jan 7, 2017 1:27 PM, "tasneem kausar"
> wrote:
>
> > Dear gromacs users
> >
> > It is first ti
hello
you may use mm/pbsa compiled with gromacs to calculate free energy
all the best
On Jan 7, 2017 1:27 PM, "tasneem kausar" wrote:
> Dear gromacs users
>
> It is first time I am trying to perform free energy calculation of protein
> and drug complex. I am following Justin' s tutorial of mehta
Dear gromacs users
It is first time I am trying to perform free energy calculation of protein
and drug complex. I am following Justin' s tutorial of mehtane in water.
That calculation are performed on a neutral system. If the ligand molecule
has charge what are the provisions that could be taken i
Dear all
It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein
Dear all
It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein
Dear all
It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein
Dear all
It is first time I am calculating free energy of protein and ligand. I am
following the Justin's tutorial of methane in water free energy
calculations. Though only van der waal lambda are defined so I have taken
the mdp files from the alchemistry.org web page. Since the ligand and
protein
Dear gxm users,
Now I am doing solvation free energy of a protein, I follow Sander Pronk's
tutorial downloaded from Gromacs page.
1. How do I check system is equilibrated?
2. I run following command
sh mklambdas.sh run.mdp topol.top equil.gro
I got following error:
mklambdas.sh: 12: mklam
Hi! Thank you for reply.
You have lost me there, tbh.
I think I didn't make it clear, I have either organic -vely changed molecule
or Cl-. Those counterbalance the +vely charged material. Therefore, I either
have organics or clorine. So, if I do TI and completely decouple vow and
charges:
couple
Hi Valentina -
Honestly, I did not get the considerations with charges. TI probably
scales interaction energies between selected groups, not charges.
Science-wise, I would first decouple organic particle, then decouple
chloride anions, and place a right sign between these two free
energies. If y
Hello,
I need an advise on how it is better to approach the ThermoD integration of
such system:
+vely charged inorganic layer, filled with water and counterbalanced by -ve
organics
Do I integrate out organics both VdW and Coulomb, making the system have
total +ve charge at lambda = 1
OR:
Do I i
On 2/20/14, 1:00 AM, Jeff Chen wrote:
Thank you very much for the quick reply.
Without using tpbconv and mdrun -rerun, I'm not sure how to get the
solute-solute energies from gromacs (please let me know it there's a way to do
this) -- since there are many more solvent molecules, the total pote
Thank you very much for the quick reply.
Without using tpbconv and mdrun -rerun, I'm not sure how to get the
solute-solute energies from gromacs (please let me know it there's a way to
do this) -- since there are many more solvent molecules, the total
potential energy is dominated by solvent-solve
On 2/19/14, 1:05 PM, Jeff Chen wrote:
Dear All,
I am trying to calculate the change in free energy that occurs when
charging multiple type B molecules in an A-B mixture. For example, I have a
mixture of 900 molecules of type A and 100 of type B. When coulomb
interactions are on, B is identical
Dear All,
I am trying to calculate the change in free energy that occurs when
charging multiple type B molecules in an A-B mixture. For example, I have a
mixture of 900 molecules of type A and 100 of type B. When coulomb
interactions are on, B is identical to A (something like TIP4P water), but
wh
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