[gmx-users] water and alkanes with Drude oscillators

[Justin Lemkul]

On 7/21/14, 10:14 AM, Yana Tsoneva wrote:
> Thanks, Justin,
>
> The .itp and .mdp files are attached here:
> https://drive.google.com/folderview?id=0B9TORs2slHYjQjY3em1mdEU3N1U&usp=sharing
> I
>   will wait for the CHARMM Drude oscillators FF to be implemented in
> GROMACS. Please, would You be so kind to notify me when it is done.
>

I will announce it's availability via this list when it is ready.

-Justin

> Best regards,
> Yana
> On 7/18/14, 7:28 AM, Yana Tsoneva wrote:
>
>> 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.
>
>
>
> Attachments are not accepted by the list.  If you wish to share files, post
> them
>
> to file-sharing services and provide a URL.
>
>
>
>> 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.
>
>>
>
>
>
> To get this to work properly, you need to implement a self-consistent force
>
> field from scratch.  Being that I can't see what you've tried (see above),
> it's
>
> hard to suggest a path forward, but as I said in my earlier message, it is
>
> currently not possible to directly use the CHARMM Drude polarizable force
> field
>
> in Gromacs (see below for my previous reply).  It will be possible sometime
> in
>
> the (relatively) near future, as I have code that will do this, but we're
>
> working out the final kinks.  The current shell code in Gromacs assumes
> massless
>
> shells, and that screws up degrees of freedom and thermostats when using
>
> mass-bearing Drude particles, which have to be treated in a special way
> within
>
> the code.
>
>
>
> -Justin
>
>
>
>> 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
>
>>
>
>>
>
>>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================