Re: [gmx-users] Restrain free energy

I assume that the motivation is that the ligand will be in the right place for binding when transforming from vacuum to protein. Maybe in this case it is ok and it's not always the case. Regarding the technical details you can try to follow the steps or wait for another response. Best,

Re: [gmx-users] Restrain free energy

Hi, You can put the numbers in https://www.wolframcloud.com/objects/asaf.farhi/test/originalDeployment and get Helmholtz free energy of restraints. Alternatively, you can remove the bond angle and dihedral angle term to get their Helmholtz/Gibbs free energies. Based on NJP A. Farhi and B.

[gmx-users] free energy of restraints

Dear Gromacs Users, Hi, we have added a free energy calculation of a dihedral restraint to the free energy website. Now it has exact analytical free energy calculations of all the restraints (can be used in absolute free energy calculations) and the standard bonded terms

[gmx-users] free energy calculator

Dear Gromacs Users, We have constructed a free-energy calculator of bonded potential terms according to the article: A. Farhi and B. Singh, New J. Phys. 18, 023039, 2016. The calculations are in principle immediate and take few seconds through the website.

[gmx-users] free energy calculator

Dear Gromacs Users, We have constructed a free-energy calculator of bonded potential terms according to the article: A. Farhi and B. Singh, New J. Phys. 18, 023039, 2016. The calculations are in principle immediate and take few seconds through the website.

Re: [gmx-users] fep protocol for gromacs 2016

Dear Yoav, Hi, did you use a soft-core technique? In which lambda range do you have large free energy differences? Best, Asaf Quoting Yoav Atsmon-Raz : Hi everyone, I’ve been trying to get a the free energy difference between a leucine residue vs an alanine

Re: [gmx-users] hydration free energy

You can also read gromacs manual. Best, Asaf Quoting asaffa...@post.tau.ac.il: Am I need to use both sc-alpha and sc-coul in that case or it is enouth to write sc-coul = no ; linear interpolation of Coulomb (none in this case) as in the mentioned tutorial? I don't

Re: [gmx-users] hydration free energy

Thanks for discussion. I am waiting already few days for anyfing reply. The technique of calculation in the file job.sh. The value of coul-λ is uniformely increasing from 0 to 1 with the step 0.02 for 50 first λ-steps and in the same way for vdw-λ last 50 λ-steps. The problem is in the last

Re: [gmx-users] hydration free energy

Am I need to use both sc-alpha and sc-coul in that case or it is enouth to write sc-coul = no ; linear interpolation of Coulomb (none in this case) as in the mentioned tutorial? I don't have experience in the parameters. You can investigate it or wait for

Re: [gmx-users] hydration free energy

Hi, Do you know which values of lambdas are used? Are you using a soft-core technique? Asaf Quoting dgfd dgdfg : Hi. I have calculated deltaG of hydration for my molecule in 101 steps. First 50 steps I decoupled coulomb interactions and last 50 - vdw. After all I

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

Hi Peng, You can compare the relative free energy with the other topology to see which order probably gives you the correct results. I don't know what is your project and for free energies associated with bonds where the atom (Carbon or Oxygen) is without nonbonded interactions there are

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

Dear Peng, There are several ways to do it. The simplest way is to take each molecule and perturb it separately. You have one Ethane molecule and one methanol molecule so you need a file containing only Ethane and a file containing only methanol. The different atoms between the molecules

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

Dear Peng, You can transform each of the molecules seperately. You can remove the nonbonded interactions of the atoms that are different between the compared molecules. Then, if you have only one dihedral relating the different atoms to the common atoms in each molecule it does not need to

[gmx-users] introduction to research on free energies

Dear Gromacs Users We would like to introduce a recently published article on calculation of relative free energies. http://www.sciencedirect.com/science/article/pii/S0010465516303411 The article includes a decoupling analysis in which the partition functions of the transformed molecules

Re: [gmx-users] Temperature interval in REMD simulations

Dear Ishrat, Roughly speaking, the temperatures should be chosen so the acceptance rates between replicas in adjacent temperatures are kept relatively constant. The high temperature should be such that k_B*T_high should be similar to the energy barriers relative to the "equilibrium state".

Re: [gmx-users] transition rate calculation

Dear Aniko, You can read http://www.sciencedirect.com/science/article/pii/S0009261497000687# For equilibrium constant you can read http://arxiv.org/abs/1502.07196 Best regards, Asaf Quoting Lábas Anikó labasan...@gmail.com: Dear Gromacs Users, Can You offer me any Gromacs tool which is

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

p.s The discussion about convergence is relevant only if Replica Exchange (H-REMD/H-PT) is used and there is a high energy barrier in the dihedral potential. If the energy barrier is not higher than ~4.5*k_B*T you are welcome to try a calculation with and without zeroing the dihedral

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

You're welcome. Please note that improper dihedral term which relates between the dummy atoms and the rest of the molecule needs to be removed (zeroed) as is explained in Section II. Thanks. Best regards, Asaf Quoting Julian Zachmann frankjulian.zachm...@uab.cat: Thanks a lot for your

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

Dear Hannes, It means that in many cases dihedral terms do not need to be transformed = not be multiplied by lambda= remain constant. Removing them also reduces the computational efficiency. The alternative is to remove them as is often done (zero them). We have shown not zero for

Re: [gmx-users] Alchemical free energy calculations - right choice of lambda points? What else might I do wrong?

Hi, It has been proven both analytically (http://arxiv.org/abs/1310.2112, Section II) and in simulations (http://arxiv.org/abs/1310.2112, Section IV and http://arxiv.org/abs/1501.01514) that the dihedral terms can remain constant in the transformation in relative free energy

Re: [gmx-users] Free energy change with harmonic restraints

Dear Natalie, The weekend was good. Thanks. I hope that you have a great weekend too. If you manage to simulate the system with restraints (A) and without restraints (B) you can calculate the free energy difference between A/B to a system in which the ligand is not interacting with the

Re: [gmx-users] Free energy change with harmonic restraints

The equations in the articles are relevant for the step Removal of Restraints in that link. Please note that these equations have been verified in http://arxiv.org/abs/1501.01514 Best regards, Asaf Quoting hannes.loeff...@stfc.ac.uk: This may be of help:

Re: [gmx-users] Free energy change with harmonic restraints

Dear Natalie, You are welcome. Could you please explain in more detail so maybe I can help? Do you want to change the strength of the restraints and measure the free energy difference associated with this change? Thanks. p.s there is also http://arxiv.org/pdf/1307.1620v7.pdf with the same

Re: [gmx-users] Free energy change with harmonic restraints

Dear Natalie, You have in http://xxx.tau.ac.il/pdf/1502.07196v3.pdf exact free energy of harmonic covalent bond and bond angle terms (or restrains). See Eqs. (2) and (3). There are also previous studies in the references there. For the dihedral term I assume it can also be calculated

Re: [gmx-users] Free energy change with harmonic restraints

Dear Natalie, What I can say is that e.g Thermodynamic Integration should give the free energy difference of this transformation. If you are interested in the free energy of binding the link provided to you by Hannes Loeffler may be useful. Also, for such a k value in case you will need