Re: [gmx-users] Relative binding free energy from a neutral to a charged molecule

] on behalf of Christopher Neale [chris.ne...@alum.utoronto.ca] Sent: 07 May 2016 06:16 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Relative binding free energy from a neutral to a charged molecule Maybe this: http://scitation.aip.org/content/aip/journal/jcp/124/22/10.1063/1.2201698

Re: [gmx-users] Relative binding free energy from a neutral to a charged molecule

<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Stefania Evoli <stefania.ev...@kaust.edu.sa> Sent: 03 May 2016 08:33:15 To: gmx-us...@gromacs.org Subject: [gmx-users] Relative binding free energy from a neutral to a charged molecule Dear Users, I’m trying to perform rela

[gmx-users] Relative binding free energy from a neutral to a charged molecule

Dear Users, I’m trying to perform relative binding free energy calculations for the transformation from a neutral to a charged molecule. I know reading several articles that this kind of transformations are affected by artifacts due to the used effective electrostatic interaction function and

Re: [gmx-users] Relative binding free energy

On Mon, 14 Mar 2016 14:08:32 + Stefania Evoli wrote: > Please, could you give a look at that? I obtained it by using the > useful tool described in the article 'A Python tool to set up > relative free energy calculations in GROMACS¹ Pavel V. Klimovich and > David

Re: [gmx-users] Relative binding free energy

Thank you for your time and precious help. The complete topology is #include "amber99sb.ff/forcefield.itp" ; Gly_GMX.top created by acpype (Rev: 403) on Wed Jan 20 13:39:56 2016 ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes

Re: [gmx-users] Relative binding free energy

I had a quick look at this and I see quite a few problems there. You don't show the [atomtypes] but I suppose that whatever you call *_dummy has zero vdW parameters. BTW, there is no need to invent different atom type names for every dummy as their non-bonded parameters are all zero anyway and

Re: [gmx-users] Relative binding free energy

The output looks like that Steepest Descents did not converge to Fmax < 100 in 2501 steps. Potential Energy = -1.80220751343547e+05 Maximum force = 1.22489147313117e+03 on atom 1 Norm of force = 1.73979807081018e+01 The structure seems not modified. When I mentioned ‘do not work’ I

Re: [gmx-users] Relative binding free energy

How does the final structure for lambda=0 minimisation look like? This may give you a hint as to what is wrong. What exactly does "do not work" mean? That's not very descriptive... It may help a lot to actually post the relevant A and B columns from your topologies. Single topology means in

Re: [gmx-users] Relative binding free energy

The minimization crush after 1182 steps like follow Step= 1116, Dmax= 1.2e-02 nm, Epot= -1.76932e+05 Fmax= 9.54828e+03, atom= 1 Step= 1117, Dmax= 1.4e-02 nm, Epot= -1.77307e+05 Fmax= 2.85691e+04, atom= 8 Step= 1119, Dmax= 8.6e-03 nm, Epot= -1.99060e+05 Fmax= 3.84768e+07, atom= 8 Step= 1124, Dmax=

[gmx-users] Relative binding free energy

Dear Users, I’m performing relative binding free energy by using Gromacs 5.0.5. As I understood reading the sections 5.3.4, 6.1 and 7.3.23 of the GROMACS 5.0.5 manual I should avoid to use couple-moltype and couple-lambda0/couple-lambda1 because they would override the A and B states, already

[gmx-users] Relative binding free energy

Dear users, I’m performing relative binding free energy calculation in Gromacs 5.0.5 of two amino acids: Alanine and Glycine. After the minimization phase the simulations crush giving me output file like 'step***.pdb' and the error is 'Fatal error: Too many LINCS warnings (1000) If you know

[gmx-users] relative binding free energy calculation Gromacs 5.0.5

Dear users, I’m performing relative binding free energy calculation in Gromacs 5.0.5. In the mdp files I’m using the following section free-energy = yes init_lambda_state= LAMBDA fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

Re: [gmx-users] relative binding free energy calculation Gromacs 5.0.5

_ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Stefania Evoli [stefania.ev...@kaust.edu.sa] Sent: 31 January 2016 12:59 To: gmx-us...@gromacs.org Subject: [gmx-users] relative binding free energy calculation Gromacs 5.0.5 Dear u