How to apply implicit solvation in gromacs ?

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Andrey Victorovich Golovin

Hi, Zhao

Implicit solvent could be set in mdp file. http://manual.gromacs.org/online/mdp_opt.html#gbsa

Lucas Zhao

Hi, Andrey

There are many options in mdp file .

But I don't know as if I need to run NVT and NPT eq.

Thanks

Hi Zhao

you are definitely need NVT

and play with electrostatics, just use trial and try approach

I will have a try

Bryce Thurston

Greetings! A few comments to add:

1. Don't use the Verlet cutoff scheme. Implicit solvent and the Verlet cutoff scheme are not compatible with one another. Newer versions of Gromacs shouldn't let you do this, but older versions (pre gromacs 5.0 I think) will run silently.

2. The general practice is to use longer cutoff lengths for non-bonded potentials in implicit solvent than would normally be used for explicit solvent. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222955/ talks a little about this.

3. Be careful with the accuracy of the results. There have been some studies in which some combinations of implicit solvent model and force field have performed well (for example):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142295/

http://dx.doi.org/10.1063/1.2161202

http://pubs.acs.org/doi/abs/10.1021/jp800282x

but others in which implicit solvent models have performed quite poorly (for example):

http://pubs.acs.org/doi/abs/10.1021/jp047126t

http://www.pnas.org/content/99/20/12777

http://pubs.acs.org/doi/abs/10.1021/jp066831u

Hi, Bryce.

I am very grateful for your reminder .

I want to apply implicit solvation in gromacs because I want to save time during MD simulation.

Zhao

Diego Prada-Gracia

Update: Implicit solvent was removed from Gromacs 2018 and later versions.

Rogelio Rodríguez-Sotres

You can have several versions of GROMACS coexisting in your computer, if you use a different installation prefix when compiling each one.

By sourcing the gromacs/bin/GMXRC you can execute several versions of gromacs on independent terminals at the same time.

in fact I have several alias in my .bashrc, that makes it very easy to activate a certain version of GROMACS.

alias gmx16_5='source /usr/local/gromacs/bin/GMXRC'

I simple type gmx16_5 on a terminal and voilá you have access to GROMACS 2016_5.

You may find usefull this paper:

Makarewicz & Kaźmierkiewicz.

DOI: 10.1007 / s00894-016-2982-4

Mangesh Damre

Diego Prada-Gracia Small correction: An implicit solvent is available for Gromacs 2018 (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#mdp-value-implicit-solvent=GBSA). It removed from later versions.

Lakshmikumar Kunche

Take a look at this .mdp file for carrying out implicit solvent simulations in gromacs. This method works well with proteins and polymers.

Gangotree Rai

Is there GB parameters are available for united atom Gromos force field?

I am not able to get it.

Amit Kumar

Lakshmikumar Kunche Sir in gromacs2018, domain decomposition need grid type neighbour search method. And again nslist=0 is not supported for grid neighbour search. So I increased the value to 5 and run but nothing happened. It was not running but terminal was busy due to it.

Later when rvdw and other radii are increased to 1.4. I was getting following error: segmentation fault (core dumped).

So please can you help?

Hi Amit, implicit solvent simulations in gromacs does not support grid neighbour search as there is no periodic boundary condition. Use neighbour grid search "simple" which will run the simulation.

A small update.

People who are all using gromacs 5.0 and above go through the link below.

https://distributedscience.wordpress.com/2017/06/18/implicit-solvent-in-gromacs/

Dear @Lakshmikumar Kunche Sir

I have tried all but got some errors. Finally, I am forced to use gromacs 4.5.5 and finally able to run implicit simulation.

Mohammad Madani

Hi Amit Kumar .

Could you please share with me your mdp file for implicit solvent remd?

Many thanks