On Thu, Dec 26, 2019 at 9:59 PM Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:
> It's Helmholtz free energy
>
Incorrect. The umbrella sampling simulations in the tutorial are performed
under an NPT ensemble. Helmholtz free energy is from an NVT ensemble, as
stated below.
-Justin
> On W
It's Helmholtz free energy
On Wed 25 Dec, 2019, 12:57 AM Souparno Adhikary,
wrote:
> Correct me if I'm wrong. I presume you are running an NPT simulation, so
> the volume doesn't need to be constant, which is a requirement for
> Helmholtz's. On contrary, Gibb's FE gives an idea of thermodynamic
Correct me if I'm wrong. I presume you are running an NPT simulation, so
the volume doesn't need to be constant, which is a requirement for
Helmholtz's. On contrary, Gibb's FE gives an idea of thermodynamic
potential (work done?).
Again, correct me if I'm wrong.
মঙ্গল, ২৪ ডিসেম্বর, ২০১৯ ৭:৫৮ PM ত
Dear all,I am using umbrella sampling tutorial (Justin tutorial). I just
wondering the binding energy is Gibbs free energy or Helmholtz free energy?and
how can I find the difference between these two free energies?
Thanks,Negar
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Hi all
I have done umbrella sampling analysis, a drug was pulled towards the CNT ans
encapsulated, then the PMF was calculated, I want to know what is the PMF in
this case, is it binding energy or energy barrier against encapsulation?
Looking forward to hearing from you
Best regards
Azadeh
--
You could either use PMF to slowly remove the peptide from the micelle or
use an absolute FEP calculation to decouple the protein interactions. PMF
may be better.
On 29 June 2016 at 21:30, Sanket Ghawali wrote:
> Dear all
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The sim
Dear all
Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns I would like to calculate the binding energy
between peptide and SDS over time.
Thanks and Regards
Sanket
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On 9/13/15 9:21 AM, Malihe Hasanzadeh wrote:
Thank you for your kind reply
Which frame or which .pdb file is useful for starting calculation?
That's only something you can answer, because you know what you've done and you
know what the reviewer is asking.
-Justin
On 13 Sep 2015 17:40, "J
Thank you for your kind reply
Which frame or which .pdb file is useful for starting calculation?
On 13 Sep 2015 17:40, "Justin Lemkul" wrote:
>
>
> On 9/13/15 8:56 AM, Malihe Hasanzadeh wrote:
>
>> Hi
>>
>> I have simulated a protein-ligand with gromacs and submitted it. My
>> reviewer asked me a
On 9/13/15 8:56 AM, Malihe Hasanzadeh wrote:
Hi
I have simulated a protein-ligand with gromacs and submitted it. My
reviewer asked me about calculation of binding energy. Which tutorial is
acceptable and suitable for me to do it?
Either free energy calculations (alchemical transformation) or
Hi
I have simulated a protein-ligand with gromacs and submitted it. My
reviewer asked me about calculation of binding energy. Which tutorial is
acceptable and suitable for me to do it?
Thank you for your help
Malihe
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On 5/8/14, 3:38 PM, Victor Sojo wrote:
Dear all,
I'm trying to determine the binding energy of a membrane protein to the
membrane. Ultimately I need to compare the binding energy of the same
protein to two similar types of lipid, the hypothesis being that there
should be a slight difference.
Dear all,
I'm trying to determine the binding energy of a membrane protein to the
membrane. Ultimately I need to compare the binding energy of the same
protein to two similar types of lipid, the hypothesis being that there
should be a slight difference.
I considered two options: alchemical transf
Thanks so much, Justin!
Your comments and paper are very helpful indeed. With "by eye" I meant I
just need to know whether one is bigger than the other, but you're complete
right: no need to speak in qualitative terms when I can quantitatively
determine DeltaDeltaG.
Thanks again!
Victor Sojo
On 2/23/14, 11:54 AM, sojovictor wrote:
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the "wrong" lipid will
imply an energetic cost.
Via umbrella sampling, I would thus
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the "wrong" lipid will
imply an energetic cost.
Via umbrella sampling, I would thus:
1) Set up a full system with protein, lip
On 2/23/14, 10:36 AM, sojovictor wrote:
Dear all,
I would like to find the difference in the energy of binding or insertion of
a protein into two different types of phospholipid membranes (plus water and
ions). i.e., my hypothesis is that the energy should be lower with one type
of membrane th
Dear all,
I would like to find the difference in the energy of binding or insertion of
a protein into two different types of phospholipid membranes (plus water and
ions). i.e., my hypothesis is that the energy should be lower with one type
of membrane than with the other.
I have considered an alc
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