[gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule

[Sandipan Dutta]

Hi Justin,

Thanks a lot for clarifying the concepts. I have searched the forums and
found which force fields would work for the polarizable models.

Best regards,
Sandipan Dutta
APCTP, South Korea


On Sat, Feb 22, 2014 at 11:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/22/14, 4:10 AM, Sandipan Dutta wrote:
>
>> Hi Justin,
>>
>> Thanks Justion for replying. I am currently simulating only 1 SWM4 water
>> molecule and I am getting a few errors.
>> I just want to clear up a few things below.
>> _____________________________________________________________________
>> *1.* when I run pdb2gmx with this .rtp file
>>
>>
>> [ SM2 ]
>>   [ atoms ]
>>    OW1    WO    1.71636     0
>>    HW2    WH    0.55733     0
>>    HW3    WH    0.55733     0
>>     DW    WD   -1.11466     0
>>     SW    WS   -1.71636     0
>>
>
> You have an error here.  The Drude (DW) and lone pair (SW?) has incorrect
> charges.  The lone pair carries a -1.11466 charge; the Drude carries
> -1.71636.
>
>
>    [ bonds ]
>>    OW1   HW2
>>    OW1   HW3
>>    OW1   DW
>>    OW1   SW
>>
>> The .gro and .top file is created but I am getting this in the terminal
>>
>> Making cmap torsions...There are    0 dihedrals,    0 impropers,    6
>> angles
>>               0 pairs,        4 bonds and     0 virtual sites
>> Total mass 18.015 a.m.u.
>> Total charge 0.000 e
>>
>> The DW and SW are virtual particles. But I am not sure why I am getting 0
>> virtual sites. Though in the log file I see 1 shell and 1 Vsite.
>>
>
> A Drude particle is not a virtual particle; it has mass and charge but
> zero LJ, making it basically just another atom.  The SWM4-NDP lone pair is
> a virtual site.
>
>  ____________________________________________________________
>> _________________
>> *2.* I read in the manual that we don't to specify the angles for
>>
>> dummy/shell particles
>> but if I keep the  OW1   DW and OW1   SW bond in .rtp file, when I run the
>> grompp
>> I get an error asking for the angles of these virtual particles. ( I found
>> that the TIP4 virtual particle
>> have some angles recorded in the [ angletypes ] section of ffbonded.itp )
>>
>> If I delete the OW1   DW and OW1   SW bonds in .rtp file
>> then the output of pdb2gmx is
>>
>> Making cmap torsions...There are    0 dihedrals,    0 impropers,    1
>> angles
>>               0 pairs,        2 bonds and     0 virtual sites
>> Total mass 18.015 a.m.u.
>> Total charge 0.000 e
>>
>> The non-hydrogen bonds are missing in the .top file and I get the error in
>> the mdrun:
>>
>> Fatal error:
>> Something weird with shells. They may not be bonded to something
>>
>> That is strange because even though I delete the .rtp bonds those bonds
>> still appear in the ffbonded.itp file.
>> So it looks like I can not delete the bonds of the virtual particles in
>> .rtp file. Is that correct?
>> ____________________________________________________________
>> ______________
>> *3.* Is this problem because of the forcefield? I am currently modifying
>> gmx.ff.
>>
>>
> Yes, almost certainly.  That force field is slated for removal because it
> is deprecated, and AFAIK is not related to SWM4 to gmx.ff in any way, so I
> doubt trying to hack it together under that force field will actually work.
>  It's fairly straightforward to implement it as part of the CHARMM Drude
> polarizable force field, which is actually what we are currently working on
> implementing in Gromacs.
>
>
> -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
>
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