Re: [gmx-users] Clarity on TI free energy terms

On Thu, 2 Jun 2016 08:27:15 + "Nash, Anthony" wrote: > Dear Hannes, > > Thanks for all the help yesterday, it helped. I, hopefully, have just > the one final question. > > I am still a little confused how Gromacs deals with the interactions > (vdW & Coul) with the

Re: [gmx-users] Clarity on TI free energy terms

Dear Hannes, Thanks for all the help yesterday, it helped. I, hopefully, have just the one final question. I am still a little confused how Gromacs deals with the interactions (vdW & Coul) with the environment when a soft-core potential has been used to switch between molecules (typeA and typeB

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 16:15:31 + "Nash, Anthony" wrote: > In the mean while, do you know of any tutorials (besides the methane > in water FE tutorial) regarding TI for amino acid substitution? I am not aware of one. You could try http://www.alchemistry.org/ > And by

Re: [gmx-users] Clarity on TI free energy terms

In the mean while, do you know of any tutorials (besides the methane in water FE tutorial) regarding TI for amino acid substitution? And by “q_off” and “vdw_on/off”, I assume you are referring to the ‘value’ of the couple-lambda0: parameter? Thanks Anthony Dr Anthony Nash Department of Chemistry

Re: [gmx-users] Clarity on TI free energy terms

Thanks for all of this material. I’ll take some time and digest what you’ve said. No doubt I’ll have a few more questions tomorrow ;-) Thanks Anthony On 01/06/2016 16:38, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler"

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 15:00:51 + "Nash, Anthony" wrote: > > This also assumes that > >you have vanishing atoms only. If you have appearing atoms only you > >would obviously have to revers the order, and when you have both you > >will have to run with two mdp/tpr setups. > >

Re: [gmx-users] Clarity on TI free energy terms

Dear Hannes, please see my comment below.. On 01/06/2016 14:45, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" wrote: >On Wed, 1 Jun 2016 12:06:20 + >"Nash, Anthony"

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 12:06:20 + "Nash, Anthony" wrote: > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 > 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 > mass_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 > 0.0 0.0 0.0

Re: [gmx-users] Clarity on TI free energy terms

Hi Hannes, Thanks for the reply. At the moment for a change in single amino acid in a triplet (a pair of triplets, showing forward and reverse change) I am settling with: vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90

Re: [gmx-users] Clarity on TI free energy terms

Set the vector to all-zeroes (or ones). On Wed, 1 Jun 2016 09:47:59 + "Nash, Anthony" wrote: > Hi Hannes, > > > Many thanks for the reply. With regards to your final comment I > understand conserving mass in theory, but I am a little confused > regarding, "keep the

Re: [gmx-users] Clarity on TI free energy terms

Hi Hannes, Many thanks for the reply. With regards to your final comment I understand conserving mass in theory, but I am a little confused regarding, "keep the mass-lambdas at one end-point as they can interact badly with constraints". I am testing pmx on a two-molecule one-system I.e., G-D2K-G

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 07:54:56 + "Nash, Anthony" wrote: > In the tutorial, charges are off in the topology and the electrostatic > coupling to lambda remains 0 throughout the 20 windows. I assume > setting col_lambdas=0 0 0 Š was for that very reason I.e., the > charges were