# Applying constraints to different molecules in a same system

**URL:** <https://gromacs.bioexcel.eu/t/applying-constraints-to-different-molecules-in-a-same-system/10586>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun, simulation-setup, topology\
**Created:** [November 19, 2024, 5:56pm UTC](https://gromacs.bioexcel.eu/t/applying-constraints-to-different-molecules-in-a-same-system/10586 "2024-11-19T17:56:33Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![abhishekchemistry](https://avatars.discourse-cdn.com/v4/letter/a/bbce88/32.png) [@abhishekchemistry](https://gromacs.bioexcel.eu/u/abhishekchemistry)\
**Post date:** [November 19, 2024, 5:56pm UTC](https://gromacs.bioexcel.eu/t/applying-constraints-to-different-molecules-in-a-same-system/10586/1 "2024-11-19T17:56:33Z")

</div>

GROMACS version: 2019.6  
GROMACS modification: Yes/No

Dear Community,

I am trying to simulate a **hydrophobic polymer** in **Madrid-2019 sulfate salt** with **TIP4P/2005 water.**

My polymer has 32 monomers connected via bonds and angles. **The bond is constrained, but the angle is not.**

Now I have the sulfate model where I have a **virtual site** and the **sulfate model is rigid**. So I use “constraints = all-angles” in the mdp file when I simulate sulfate + water (no polymer) and it works perfectly.

But now when I want to simulate the polymer + sulfate + water, I want to keep the angles of the polymer flexible and the bonds of the polymer constrained and also keeping all the bonds and angles constrained in the sulfate. How do I do that? So far I could not find any solution. Any help would be appreciated. Thank you. I attach the topology here for convenience.

**1. Polymer**

[moleculetype]  
; Name nrexcl  
POL 2

[atoms]  
; nr type resnr resid atom cgnr charge mass  
1 P 1 POL P 1 0.000 14.0270  
2 P 1 POL P 2 0.000 14.0270  
3 P 1 POL P 3 0.000 14.0270  
4 P 1 POL P 4 0.000 14.0270  
5 P 1 POL P 5 0.000 14.0270  
6 P 1 POL P 6 0.000 14.0270  
7 P 1 POL P 7 0.000 14.0270  
8 P 1 POL P 8 0.000 14.0270  
9 P 1 POL P 9 0.000 14.0270  
10 P 1 POL P 10 0.000 14.0270  
11 P 1 POL P 11 0.000 14.0270  
12 P 1 POL P 12 0.000 14.0270  
13 P 1 POL P 13 0.000 14.0270  
14 P 1 POL P 14 0.000 14.0270  
15 P 1 POL P 15 0.000 14.0270  
16 P 1 POL P 16 0.000 14.0270  
17 P 1 POL P 17 0.000 14.0270  
18 P 1 POL P 18 0.000 14.0270  
19 P 1 POL P 19 0.000 14.0270  
20 P 1 POL P 20 0.000 14.0270  
21 P 1 POL P 21 0.000 14.0270  
22 P 1 POL P 22 0.000 14.0270  
23 P 1 POL P 23 0.000 14.0270  
24 P 1 POL P 24 0.000 14.0270  
25 P 1 POL P 25 0.000 14.0270  
26 P 1 POL P 26 0.000 14.0270  
27 P 1 POL P 27 0.000 14.0270  
28 P 1 POL P 28 0.000 14.0270  
29 P 1 POL P 29 0.000 14.0270  
30 P 1 POL P 30 0.000 14.0270  
31 P 1 POL P 31 0.000 14.0270  
32 P 1 POL P 32 0.000 14.0270

[bonds]  
; ai aj fu b0 kb  
1 2 1 0.1530 330000.0  
2 3 1 0.1530 330000.0  
3 4 1 0.1530 330000.0  
4 5 1 0.1530 330000.0  
5 6 1 0.1530 330000.0  
6 7 1 0.1530 330000.0  
7 8 1 0.1530 330000.0  
8 9 1 0.1530 330000.0  
9 10 1 0.1530 330000.0  
10 11 1 0.1530 330000.0  
11 12 1 0.1530 330000.0  
12 13 1 0.1530 330000.0  
13 14 1 0.1530 330000.0  
14 15 1 0.1530 330000.0  
15 16 1 0.1530 330000.0  
16 17 1 0.1530 330000.0  
17 18 1 0.1530 330000.0  
18 19 1 0.1530 330000.0  
19 20 1 0.1530 330000.0  
20 21 1 0.1530 330000.0  
21 22 1 0.1530 330000.0  
22 23 1 0.1530 330000.0  
23 24 1 0.1530 330000.0  
24 25 1 0.1530 330000.0  
25 26 1 0.1530 330000.0  
26 27 1 0.1530 330000.0  
27 28 1 0.1530 330000.0  
28 29 1 0.1530 330000.0  
29 30 1 0.1530 330000.0  
30 31 1 0.1530 330000.0  
31 32 1 0.1530 330000.0

[angles]  
; ai aj ak fu theta0 ktheta  
1 2 3 2 111.000 100.000  
2 3 4 2 111.000 100.000  
3 4 5 2 111.000 100.000  
4 5 6 2 111.000 100.000  
5 6 7 2 111.000 100.000  
6 7 8 2 111.000 100.000  
7 8 9 2 111.000 100.000  
8 9 10 2 111.000 100.000  
9 10 11 2 111.000 100.000  
10 11 12 2 111.000 100.000  
11 12 13 2 111.000 100.000  
12 13 14 2 111.000 100.000  
13 14 15 2 111.000 100.000  
14 15 16 2 111.000 100.000  
15 16 17 2 111.000 100.000  
16 17 18 2 111.000 100.000  
17 18 19 2 111.000 100.000  
18 19 20 2 111.000 100.000  
19 20 21 2 111.000 100.000  
20 21 22 2 111.000 100.000  
21 22 23 2 111.000 100.000  
22 23 24 2 111.000 100.000  
23 24 25 2 111.000 100.000  
24 25 26 2 111.000 100.000  
25 26 27 2 111.000 100.000  
26 27 28 2 111.000 100.000  
27 28 29 2 111.000 100.000  
28 29 30 2 111.000 100.000  
29 30 31 2 111.000 100.000  
30 31 32 2 111.000 100.000

**3. Sulfate**

[moleculetype]  
; name nrexcl  
SO4 1

[atoms]  
;nr type resnr residu atom cgnr charge  
1 OSO4 1 SO4 O1 1 -0.65 24.01565  
2 OSO4 1 SO4 O2 1 -0.65 24.01565  
3 OSO4 1 SO4 O3 1 -0.65 24.01565  
4 OSO4 1 SO4 O4 1 -0.65 24.01565  
5 SSO4 1 SO4 S5 1 0.9 0.0

[constraints]  
;i j funct dist  
; dist\_OX=0.149; dist\_XX=2\*sqrt(2/3)\*dist\_OX  
1 2 1 0.243316  
1 3 1 0.243316  
1 4 1 0.243316  
2 3 1 0.243316  
2 4 1 0.243316  
3 4 1 0.243316

[exclusions]  
1 2 3 4 5  
2 1 3 4 5  
3 1 2 4 5  
4 1 2 3 5  
5 1 2 3 4

[virtual\_sitesn]

; Site funct from  
5 1 1 2 3 4

Best,  
Abhishek