- Posts: 15
What type of CG particle is suitable for CNTs?
- exianshine
-
Topic Author
- Offline
- Fresh Boarder
Less
More
11 years 5 months ago #1266
by exianshine
What type of CG particle is suitable for CNTs? was created by exianshine
I wonder what is the proper CG beads type for a CNT?
I find in Prof. Sansom's paper that C1 is used, and there is also some others using SC4 or SC1(J. Phys. Chem. C 2012, 116, 9327−9333), what kind of beads is best for CNTs.
What if I want to change the CNT to particles that they possess charges? is Q0 type is OK?
And what's more, I want to use PME to calculate the electrotic interaction, is it OK?
Thanks a lot.
I find in Prof. Sansom's paper that C1 is used, and there is also some others using SC4 or SC1(J. Phys. Chem. C 2012, 116, 9327−9333), what kind of beads is best for CNTs.
What if I want to change the CNT to particles that they possess charges? is Q0 type is OK?
And what's more, I want to use PME to calculate the electrotic interaction, is it OK?
Thanks a lot.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 5 months ago #1271
by djurre
Replied by djurre on topic What type of CG particle is suitable for CNTs?
What kind of molecule is CNT?
There are some discussions on the forum, eg: md.chem.rug.nl/cgmartini/index.php/user-...m/forum/topic?id=140
There are some discussions on the forum, eg: md.chem.rug.nl/cgmartini/index.php/user-...m/forum/topic?id=140
Please Log in or Create an account to join the conversation.
- exianshine
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 15
11 years 5 months ago #1274
by exianshine
Replied by exianshine on topic What type of CG particle is suitable for CNTs?
Thanks for your reply. I know it's dangerous to use PME in Martini force field. But I have to consider the long range electrotic interactions. So what could I do to confirm that my system is OK with PME? Fro example, what could be analysed to prove the use of PME is fine.
I find a martini ff with a particle type of CNP in the itp files. So I think it may be the right choice of CG CNT particles.
However, what if I want to change the CNT to some other NTs that they have net charges on the surface. I found that there is no SQ0, SQa, SQd or SQad defined as SP1, SC1 for the ring type of CG bead? Do I have to choose the Q0 ? is it proper since the mass of Q0 is not 48 as in S** type of beads.
I find a martini ff with a particle type of CNP in the itp files. So I think it may be the right choice of CG CNT particles.
However, what if I want to change the CNT to some other NTs that they have net charges on the surface. I found that there is no SQ0, SQa, SQd or SQad defined as SP1, SC1 for the ring type of CG bead? Do I have to choose the Q0 ? is it proper since the mass of Q0 is not 48 as in S** type of beads.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 5 months ago #1276
by djurre
Replied by djurre on topic What type of CG particle is suitable for CNTs?
For the PME you should check for artifacts, such as unexpected expansion of you system in one dimension or the cluster/freezing of ions.
Where do you find the CNP/CNT particles? In which molecules are they used? In which itp file are they defined?
Where do you find the CNP/CNT particles? In which molecules are they used? In which itp file are they defined?
Please Log in or Create an account to join the conversation.
- exianshine
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 15
11 years 5 months ago #1277
by exianshine
Replied by exianshine on topic What type of CG particle is suitable for CNTs?
I found it in the "example applications" in this site. in the files for Fullerenes, there is itp files named "martini_v2.1_CNT.itp"
is it suitable for CNT coarse grained beads?
Is "Q0" type bead suitable for chaeged nanotube beads?
is it suitable for CNT coarse grained beads?
Is "Q0" type bead suitable for chaeged nanotube beads?
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
11 years 5 months ago #1278
by jaakko
Replied by jaakko on topic What type of CG particle is suitable for CNTs?
The CNP bead type is based on SC4 if I recall correctly. The "martini_v2.1_CNT.itp" does not have SQx bead types but you could probably get started by defining CNP to interact with them in the same way as SC4.
The paper related to the CNP bead type (dx.doi.org/10.1021/ct3000102) comments also on CNT parameters and argues why CNP or SC4 could be a reasonable starting point for them. Validation against experimental data would settle the bead type selection but apparently getting experimental data on CNTs is difficult.
The choice of bead types for charged residues on the NT surface really depends on the residue. Consider your mapping and the hydrogen bonding capabilities when selecting the bead types. Again, optimally you want to validate your bead type selection by comparing to experiment if that's possible.
The paper related to the CNP bead type (dx.doi.org/10.1021/ct3000102) comments also on CNT parameters and argues why CNP or SC4 could be a reasonable starting point for them. Validation against experimental data would settle the bead type selection but apparently getting experimental data on CNTs is difficult.
The choice of bead types for charged residues on the NT surface really depends on the residue. Consider your mapping and the hydrogen bonding capabilities when selecting the bead types. Again, optimally you want to validate your bead type selection by comparing to experiment if that's possible.
Please Log in or Create an account to join the conversation.
Time to create page: 0.106 seconds