- Posts: 2
PMP membrane
- gvdmm
-
Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 11 months ago #8932
by gvdmm
PMP membrane was created by gvdmm
Hi, I have been trying to model PMP membranes with some nanoparticles in them, however when I try to anneal them I get:
Step 15: The total potential energy is nan, which is not finite. The LJ and
electrostatic contributions to the energy are 0 and 0, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.
To solve this issue, the team believed that increasing the rvdw would be ideal, however, it seems that martini was not made for anything greater than 1.2. Does anyone have any suggestions?
Step 15: The total potential energy is nan, which is not finite. The LJ and
electrostatic contributions to the energy are 0 and 0, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.
To solve this issue, the team believed that increasing the rvdw would be ideal, however, it seems that martini was not made for anything greater than 1.2. Does anyone have any suggestions?
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
2 years 10 months ago #8963
by riccardo
Replied by riccardo on topic PMP membrane
What does PMP mean? How did you build the system? What's your annealing protocol? Most of the times these issues have to do with poor equilibration or poor annealing protocol (e.g., you jump too quickly from e.g. 300K to 700K).
By rvdw you mean the cutoff of the force field - why would that help?
By rvdw you mean the cutoff of the force field - why would that help?
Please Log in or Create an account to join the conversation.
- gvdmm
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 2
2 years 10 months ago #8975
by gvdmm
Replied by gvdmm on topic PMP membrane
Thank you for your response. Firstly, PMP is poly(4-methyl-2-pentyne). SecondIy I personally did not build the system, but if I am not mistaken, my lab-mates built it in Material Studio and they mapped it to course grain (I don't have the mapping, now, but I could probably get it, if it helps). Third, our file that conducts the annealing contains:
integrator = md
dt = 0.001
nsteps = 5000000
nstcomm = 100
.
.
.
cutoff-scheme = Verlet
coulombtype = Cut-off ;Reaction_field ;For use with Verlet-pairlist
rcoulomb_switch = 0.0
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Cut-off ;cutoff ;For use with Verlet-pairlist
rvdw_switch = 0.9
vdw-modifier = Potential-shift-Verlet
rvdw = 1.2
.
.
.
annealing = single
annealing-npoints = 6
annealing-time = 0 300 400 1000 1100 1200
annealing-temp = 300 300 500 500 300 300
I can offer more information on the protocol, if it helps on another post. And finally, I speculate that the bonded atoms are moving too far apart for the force-field and, thus, the error, but I may as well be completely wrong. I just know that when we increased the value the error disappeared.
integrator = md
dt = 0.001
nsteps = 5000000
nstcomm = 100
.
.
.
cutoff-scheme = Verlet
coulombtype = Cut-off ;Reaction_field ;For use with Verlet-pairlist
rcoulomb_switch = 0.0
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Cut-off ;cutoff ;For use with Verlet-pairlist
rvdw_switch = 0.9
vdw-modifier = Potential-shift-Verlet
rvdw = 1.2
.
.
.
annealing = single
annealing-npoints = 6
annealing-time = 0 300 400 1000 1100 1200
annealing-temp = 300 300 500 500 300 300
I can offer more information on the protocol, if it helps on another post. And finally, I speculate that the bonded atoms are moving too far apart for the force-field and, thus, the error, but I may as well be completely wrong. I just know that when we increased the value the error disappeared.
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
2 years 10 months ago #8996
by riccardo
Replied by riccardo on topic PMP membrane
Is this a polymeric system? How are you mapping poly(4-methyl-2-pentyne) (i.e., how many beads describe poly(4-methyl-2-pentyne) and if it's polymerized, how many do you have connected and how do you connect them)?
If the initial mapping of the system generated at the atomistic level with Material Studio is very far off from a Martini minimum, then you're gonna have problems. Actually, did you first energy minimize and equilibrate the CG system? Does that work OK?
If the initial mapping of the system generated at the atomistic level with Material Studio is very far off from a Martini minimum, then you're gonna have problems. Actually, did you first energy minimize and equilibrate the CG system? Does that work OK?
Please Log in or Create an account to join the conversation.
Time to create page: 0.087 seconds