[gmx-users] water and alkanes with Drude oscillators

[Yana Tsoneva]

Dear colleagues,



I am dealing with systems consisting of water/different oils. I am 
using Gromacs-4.6.5. I have wrote to You twice about my problems (You can 
find my previous messages and their answers below), but I still can not deal 

with them.

Until now I ran my simulations with TIP4P water model and AMBER99 FF 
for the alkanes. First I wrote to You because I wanted to simulate 
polarizable water with non-polarizable alkanes, but I understood that I can 
not do it.

This is why I tried to simulate SWM4-NDP that has to be consistent with 
CHARMM FF (for wich there are implemented Drude oscillators), the .itp and 
.mdp files of which are attached. Obviously, there is a problem with the 
parameters I use, but I do not know where exactly it is. This is why I am 
turning to You for help.
In addition, I still can not understand how I can use CHARMM FF with 
massless Drude oscillators with SWM4-NDP (I think its Drude particle is 
massless as well) in Gromacs.

Please, explain to me how to do it, because I am totally lost.

Looking forward to your reply,
Yana

On 7/9/14, 3:56 AM, Yana Tsoneva wrote:

> Dear colleagues,

>

> I am running simulations using Gromacs - 4.6.5 and my systems consist of

> water/different oils. Until now I have used TIP4P water model and amber99

> for the alkanes.

>

> I need to run the same simulations, but with a polarizable water model. I

> succeeded in simulating pure polarizable water (sw-rigid of van Gusteren),

> but now I have problems adding the alkanes. I know that I should not mix

> different force fields, but is there any chance for me to simulate

> polarizable water and non-polarizable alkanes? If there is one, can you 
tell

> me how to do it? I read that there is a modification of the CHARMM force

> field to simulate alkanes with Drude oscillators. Is this the way to 
achieve

> compatibility of the force fields?

>



The CHARMM Drude FF for alkanes was parametrized against SWM4-DP, not SW, so 


such a combination is not valid.  You need a self-consistent force field.  I 


doubt that an additive model of alkanes in conjunction with a polarizable 
model 

of water would be reliable.



-Justin

On 7/14/14, 6:17 AM, Yana Tsoneva wrote:

> Dear colleagues,

>

>

>

> Firstly, I want to thank Justin Lemkul for helping me on the topic

> "polarizable water and non-polarizable alkanes". Now I have to

> simulate systems that consist of polarizable water and polarizable 
alkanes.

> The chosen force field is CHARMM with Drude oscillators.

>

> I am trying to use the python script cgenff_charmm2gmx.py to generate the

> needed files, but the following error occurs:

>

>

>

> NOTE1: Code tested with python 2.7.3. Your version: 2.6.6 (r266:84292, Jan

> 22 2014, 09:42:36)

>

> [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

>

> NOTE2: Please be sure to use the same version of CGenFF in your 
simulations

> that was used during parameter generation:

>

> --Version of CGenFF detected in  charmm36-mar2014.ff//forcefield.doc :

> 2b8

>

> NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include

> parameters that are already in CGenFF' option when uploading a molecule 
into

>

> CGenFF.

>

> error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top

>

> 17 0

>

>

>

> I found that another person had this problem, but I still could not fix 
it.

> I have attached the files I am using. The command line I enter is:

>

> ./cgenff_charmm2gmx.py PENT pentane.mol2

> ./drude_toppar_oct13/toppar_drude_model_2013a.str charmm36-mar2014.ff

>

>

>

> I will really appreciate if someone could help me,

>



The CGenFF conversion script is intended to process a .mol2 file with a 
single 

molecule and a corresponding .str file with a single molecule.  What you're 

trying to do is doomed to fail for two reasons:



1. The toppar_drude_model_2013a.str file contains all model compounds we 
used in 

the parametrization of the Drude FF

2. CHARMM36 from March 2014 is an additive force field.



Please also note that our parametrization of the Drude FF is with 
thermalized, 

mass-bearing Drude particles.  In principle, these types of systems can be 

simulated in Gromacs using an SCF procedure to solve the positions of the 
Drude 

particles, but not out of the box in the case of mass-bearing Drudes.  I am 

working on implementing all of the necessary algorithms to make this a 
reality, 

but the code is not yet suitable for public consumption.  Using massless 

Drudes/shells will work fine, but strictly speaking that is not the Drude FF 


that we have parametrized.



-Justin