normal CHOL with virtual sites

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4 months 1 week ago #7651 by dariush
dariush created the topic: CHOL with virtual sites
Hello,

Could you please let me know what is the meaning of this part of CHOL's forcefield?

#ifdef FLEXIBLE
1 3 1 0.4904 1000000
1 4 1 0.6019 1000000
3 4 1 0.2719 1000000
7 3 1 0.7237 1000000
7 4 1 0.5376 1000000
#else
[ constraints ]
1 3 1 0.4904
1 4 1 0.6019
3 4 1 0.2719
7 3 1 0.7237
7 4 1 0.5376
#endif

Thanks!
Dariush

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4 months 1 week ago #7652 by dariush
dariush replied the topic: CHOL with virtual sites
I have another question too. I am working to build a model for beta-sitosterol. The only difference between these molecules is related to an extra ethyl group in beta-sitosterol:
goo.gl/sgSC84


Here is what I put together to start. Could you please let me know if I am approaching the right answer?



[ moleculetype ]
; molname nrexcl
BSTL 1

[ atoms ]
; i type resnr residue atom cgnr charge mass
1 SP1 1 BSTL ROH 1 0.0 77.22
2 SC1 1 BSTL R1 2 0.0 0.0
3 SC3 1 BSTL R2 3 0.0 38.69
4 SC1 1 BSTL R3 4 0.0 159.65
5 SC1 1 BSTL R4 5 0.0 0.0
6 SC1 1 BSTL R5 6 0.0 0.0
7 SC1 1 BSTL C1 7 0.0 39.44
8 C1 1 BSTL C2 8 0.0 72.0
9 C1 1 BSTL C3 8 0.0 72.0 ; added

[ bonds ]
; i j funct length force
7 8 1 0.425 1250.0
7 9 1 0.425 1250.0 ; added
#ifdef FLEXIBLE
1 3 1 0.4904 1000000
1 4 1 0.6019 1000000
3 4 1 0.2719 1000000
7 3 1 0.7237 1000000
7 4 1 0.5376 1000000
#else
[ constraints ]
1 3 1 0.4904
1 4 1 0.6019
3 4 1 0.2719
7 3 1 0.7237
7 4 1 0.5376
#endif

[ dihedrals ]
1 3 4 7 2 -179.7 50

[ virtual_sites3 ]
; In-plane bead from frame 4-3-7 (bead 5)
5 4 3 7 1 0.9613 0.6320
; Out-of-plane bead from frame 3-1-4 (bead 2)
2 3 1 4 4 0.5207 0.2882 -0.83824
; Out-of-plane bead from frame 4-3-7 (bead 6)
6 4 3 7 4 0.2287 0.4111 1.1531

[ angles ]
; i j k funct angle force
4 7 8 2 120.0 45.0 ; changed from 25 --> to 45
4 7 9 2 120.0 45.0 ; added

[ exclusions ]
; i j k ...
1 2 3 4 5 6 7 8 ; added 8 to each line and added one line to the end
2 3 4 5 6 7 8
3 4 5 6 7 8
4 5 6 7 8
5 6 7 8
6 7 8
7 8

Thanks for your help, as always!!

Dariush

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4 months 1 week ago #7655 by helgi
helgi replied the topic: CHOL with virtual sites
If you add the -DFLEXIBLE flag to your .mdp file e.g.:
define = -DFLEXIBLE

Then the constraints are changed into stiff bonds. This can be very helpful if your initial structure is not exact to help with minimization, but after that they should be changed back to constraints for better stability.

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4 months 1 week ago #7656 by helgi
helgi replied the topic: CHOL with virtual sites
As for the beta-sitosterol.
Yes, you can use the regular cholesterol structure and add to it, but as you are adding only x2 carbons you can't just added a regular bead (~4 heavy atoms).
Probably best to use the current cholesterol up to bead 7 then replace the "tail" with x2 s beads. As these are not straight carbon chains the bonds / angles between them will be none standard and should be measured from reference anatomist simulations.

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4 months 1 week ago #7662 by dariush
dariush replied the topic: CHOL with virtual sites
Thank you, Helgi, for both responses!


For beta-sitosterol, I assume you meant adding two C2 type beads - am I right? If so, it is a sensible suggestion.

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