[gmx-users] FW: Free energy of solvation using the Bar method

[Innocenti Malini, Riccardo]

Hi Shekhovtsov,

Thank you very much. 

Kind regards,
Riccardo

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Artem Shekhovtsov
Sent: Monday, June 3, 2019 4:39 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] FW: Free energy of solvation using the Bar method

Hello,
Try to swap vdw_lambdas and coul_lambdas in *.mdp file like this:
coul_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 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00
vdw_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00  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

Possible explanation:
http://www.alchemistry.org/wiki/Constructing_a_Pathway_of_Intermediate_States#Avoid_turning_off_charges_and_Lennard-Jones_sites_at_the_same_time

Best regards,
Shekhovtsov Artem

On Mon, Jun 3, 2019 at 5:23 PM Innocenti Malini, Riccardo < Riccardo.InnocentiMalini at empa.ch> wrote:

>
> Dear all,
>
> I am currently trying to calculate the free energy of solvation for a 
> small hydrophobic molecule in water using the OPLSaa force field, 
> however for vdw lambda values above 0.2 my system continuously explodes.
>
> Before starting the free energy calculations I equilibrated the system
> (100 ps in NVT and 4 ns in NPT ensemble). Then before starting the 
> free energy calculations before each lambda point I minimized the 
> energy using first the steepest descent method and then L-BFGS. The 
> system is then simulated in the NVT ensemble where it tends to blows 
> when the vdw for Lambda = 0.3. Below this value the system works fine 
> in simulations of up to 8 ns and the system appears to be equilibrated.
>
> I am not sure why this is happening. Would anybody have any advice? 
> Here is the free energy section of the mdp file:
>
> free_energy              = yes
> couple-moltype           = Other
> couple-lambda0           = vdw-q
> couple-lambda1           = none
> couple-intramol          = no
> init-lambda              = -1
> init_lambda_state        = 3
> delta_lambda             = 0
> nstdhdl                  = 10
> fep-lambdas              =
> mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00
> coul_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 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
> 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 1.00 1.00 
> 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 
> 1.00
> 1.00 1.00
> bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00
> restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00
> temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
> 0.00
> 0.00 0.00
> calc_lambda_neighbors    = 1
> init-lambda-weights      =
> dhdl-print-energy        = no
> sc-alpha                 = 0.5
> sc-power                 = 1
> sc-r-power               = 6
> sc-sigma                 = 0.3
> sc-coul                  = no
> separate-dhdl-file       = yes
> dhdl-derivatives         = yes
> dh_hist_size             = 0
> dh_hist_spacing          = 0.1
>
> Thank you in advance for your help.
>
> Kind regards,
> Riccardo
>
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