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

Sandipan Dutta sandy0207 at gmail.com
Sat Feb 22 10:10:21 CET 2014

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
 [ 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.
*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
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

In case I keep all the bonds in the .rtp files and put all the angles even
for the virtual particles in the ffbonded and run
mdrun I get Segmentation fault.

Can you please help me with this?

Thanks a lot again in advance.

Sandipan Dutta
APCTP, South Korea.


On Fri, Feb 21, 2014 at 10:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 2/21/14, 2:57 AM, Sandipan Dutta wrote:
>> Dear GMX users:
>> Thanks Justin for the reply. Yes there was a problem in the topology file
>> .rtp.
>> I am modifying the gmx.ff force field files. I have obtained swm4.itp
>> from the
>> gromacs link
>> URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-
>> users/attachments/20110808/9d18f222/attachment.html>
>>   Although I added the bond information in the ffbonded.itp file, I
>> forgot to
>> add the bond between the oxygen and the Drude particle in the .rtp file (
>> I
>> followed the TIP4 water model which does not seem to have a bond with the
>> IW
>> particle and oxygen). But when I run the grompp I get an error
>> ERROR 3 [file topol.top, line 48]:
>>    No default Angle types
>> This is because of the fact that I have not provided the angle between
>> the Drude
>> particle and the oxygen in the [ angletypes ] section of the ffbonded.itp
>> file.
>> I thought that since the bond length of Oxygen-Drude particle is zero we
>> do not
>> need the angle. How do I avoid mentioning the angle in ffbonded.itp?
> There are no angle parameters involving Drudes or virtual sites.  In
> theory, since you've provided an angle type for it, there should be no
> problem, but the only defined angle should be H-O-H.
> -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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