[gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119

[Groenhof, Gerrit]

Hi,

Indeed, Link atoms have to be added to the .gro file. The atom indexing in the .gro file is not used, so no need to renumber. A simple editconf can do that for you if too, if you would like to have the numbering correct.  However, you need to adjust the total number of atoms at the top of the .gro file. 

for the bonded interactions, you should remove the gb_x , because these defines contain the bond type information as well. Easiest is to add a ';' like this 

1851  1853     2   ; gb_10

which means that what comes after is ignored.

good luck,

Gerrit

Message: 3
Date: Thu, 21 Apr 2016 17:43:47 +0900
From: bharat gupta <bharat.85.monu at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Defining LA atoms in .gro file
Message-ID:
        <CAAh+zSV7BrctXYs0=yoAekVnFbxeES+c0zTxODqA8jGin10ysQ at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear GMX Users,

I am trying to perform QM/MM simulation for my system and I need to define
LA for the boundary between QM and MM region. I have the boundary regions
but I don't know how to add them in the gro file. Do I have to manually
modify the .gro file, if that's the case, adding, them manually how do I
renumber the rest of the atoms and residues? Here's what I have done:

 3715YWR   H21 3562   4.283   4.647   4.755 -1.1354  1.0843 -0.8713
  372XXX     LA 3563   2.475   3.856   2.040 -0.0020 -0.1066  0.1995
  373XXX     LA 3564   0.475   3.856   2.040 -0.0020 -0.1066  0.1995
  374XXX     LA 3565   1.475   3.856   2.040 -0.0020 -0.1066  0.1995
  375XXX     LA 3566   3.475   3.856   2.040 -0.0020 -0.1066  0.1995
  376XXX     LA 3567   0.875   3.856   2.040 -0.0020 -0.1066  0.1995
  377XXX     LA 3568   1.575   3.856   2.040 -0.0020 -0.1066  0.1995
  372SOL     OW 3563   3.414   3.445   2.243 -0.1786 -0.5561  0.4692
  372SOL    HW1 3564   3.479   3.440   2.167  0.5613 -1.1084  1.1215
  372SOL    HW2 3565   3.329   3.488   2.212  0.4389  0.0440 -0.4374
  373SOL     OW 3566   1.589   3.334   2.348  0.6300  0.1793 -0.1279
  373SOL    HW1 3567   1.639   3.413   2.384  1.2205  0.0166 -0.5746
  373SOL    HW2 3568   1.588   3.337   2.248 -1.5585  0.9770 -0.1508
  374SOL     OW 3569   5.280   6.227   4.070  0.5862 -0.1571 -0.6930

So, I added the LA atoms between atom no H21/3562 and OW/3563 manually.
Please let me whether this is the correct way of adding the LA atoms ?

Also, I need to modify the bond_types as well in the topology file to 5. Is
this the correct way:

1851  1853     2    gb_10
 1853  1854     5    gb_2
 1853  1855     5    gb_21
 1855  1856     5    gb_27
 1855  1862     5    gb_27
 1856  1857     5    gb_27
 1857  1858     5    gb_27
 1858  1859     5    gb_5
 1858  1860     5    gb_13
 1860  1861     5    gb_1
 1862  1863     5    gb_5
 1862  1864     2    gb_10
 1864  1865     2    gb_2

I haven't changed the values for C0 for the QM atoms but I have changed
their type to 5.

--
*Best Regards*
BM