Re: [gmx-users] Perturbation Thermodynamic Integration

What I notice is: You don't use bond-constraints but you have set your time step to 2 fs. What happens if you (significantly) increase simulation time per lambda? Your variances are really large. What is the motivation of using such a long cutoff radius for vdW? On Fri, 26 May 2017 11:13:08

Re: [gmx-users] Perturbation Thermodynamic Integration

Hello, I've run Gromacs following the suggestions, but I still get nonzero contributions from the mass changing. I will outline in-depth what I did. Thank you very much for your help! (1) Heptane molecule was inserted into a box of size 10x10x10 nm3 with 7833 water molecules using Gromacs

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, 16 May 2017 15:13:10 -0400 Dan Gil wrote: > If you do this via decoupling ("absolute" transformation) you do that > > once for molecule A and once for molecule B. > > > I believe you are referring to the BAR method? I am trying to see if > I get the same

Re: [gmx-users] Perturbation Thermodynamic Integration

> > What does grompp from 2016.3 report? > ERROR 1 [file topol.top, line 10]: Atom 1 in molecule type 'HEPT' has different A and B state charges and/or atom types set in the topology file as well as through the mdp option 'couple-moltype'. You can not use both these methods simultaneously.

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, 16 May 2017 10:28:08 -0400 Dan Gil wrote: > Thank you for the advice on the cut-off schemes and PME methods. > > What is the physical meaning of a non-interacting final state > > that has different masses from the initial state? > > > These free energy options

Re: [gmx-users] Perturbation Thermodynamic Integration

Thank you for the advice on the cut-off schemes and PME methods. What is the physical meaning of a non-interacting final state > that has different masses from the initial state? These free energy options was just from me trying to figure out why mass has any contributions at all. I am going

Re: [gmx-users] Perturbation Thermodynamic Integration

I have not really followed the previous email exchange but from this mdp file I wonder what you are trying to achieve. You seem to want to decouple all atoms of your HEPT molecule (couple-moltype, couple-intramol) from its environment but then you also change the masses. What is the physical

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, May 16, 2017 at 3:54 PM Dan Gil wrote: > Hi, > > The latest version of Gromacs I have is 5.1. Using this version, grompp > produces no warnings or errors. > I know you won't get the new warning from the old code ;-) You'd need the latest grompp, as I've mentioned

Re: [gmx-users] Perturbation Thermodynamic Integration

On 5/16/17 9:53 AM, Dan Gil wrote: Hi, The latest version of Gromacs I have is 5.1. Using this version, grompp produces no warnings or errors. I am using OPLS-AA, and I didn't have any issues with it thus far. I inherited this research project though 3 years ago. Is there something you think

Re: [gmx-users] Perturbation Thermodynamic Integration

Hi, The latest version of Gromacs I have is 5.1. Using this version, grompp produces no warnings or errors. I am using OPLS-AA, and I didn't have any issues with it thus far. I inherited this research project though 3 years ago. Is there something you think I should look at with scrutiny? On

Re: [gmx-users] Perturbation Thermodynamic Integration

Hi, Yes that looks like it is the envelope of the new warning. What does grompp from 2016.3 report? (Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd reject that method immediately unless there was evidence that it worked well for a range of observables, and was consistent

Re: [gmx-users] Perturbation Thermodynamic Integration

Sorry, here is the mdp file: ;Integration Method and Parameters integrator = sd nsteps = 10 dt = 0.002 nstenergy= 1000 nstlog = 5000 ;Output Control nstxout = 0 nstvout = 0 ;Cutoff Schemes cutoff-scheme= group

Re: [gmx-users] Perturbation Thermodynamic Integration

Hi, What use are you making of constraints? Justin suggested sharing a full mdp file, which I think may help. We discovered last year that you can get equipartition failure for (IIRC) all-bonds constraints for moieties like -CH2Cl, and latest grompp now detects this. Mark On Tue, 16 May 2017

[gmx-users] Perturbation Thermodynamic Integration

Hello, The last thread was getting too big, and the conversation evolved to a topic different from my original question, so I decided to start a new thread. We were discussing thermodynamic integration, and why the mass_lambdas would have any contribution to the derivative of the Hamiltonian. I