[gmx-users] water and alkanes with Drude oscillators
fhyt at chem.uni-sofia.bg
Fri Jul 18 13:28:45 CEST 2014
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
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,
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
> 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
> 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
of water would be reliable.
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
> 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
> that was used during parameter generation:
> --Version of CGenFF detected in charmm36-mar2014.ff//forcefield.doc :
> NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
> parameters that are already in CGenFF' option when uploading a molecule
> 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
> 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
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
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
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
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
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.
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