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Strange behaviour @ ~3ns for ~40 residue protein
- johnny
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13 years 2 months ago #557
by johnny
Strange behaviour @ ~3ns for ~40 residue protein was created by johnny
hello,
i have a ~40 residue protein that i am trying to simulate with MARTINI. i ran a 100ns simulation that had previously worked on a ~140 residue protein. at about 3ns the potential energy plummets, rmsd becomes nearly a flat line. i'm using a dt of 20fs and the non-polarizable water. here is my .mdp:
; Run parameters
integrator = md
nsteps = 5000000
dt = 0.02
tinit = 0
nstcomm = 1
comm_mode = linear
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstxtcout = 1000
xtc_precision = 1000
nstenergy = 1000
; Bond parameters
constraints = none
constraint_algorithm = lincs
lincs_order = 4
lincs_warnangle = 30
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.4
rcoulomb = 1.2
epsilon_r = 15
rvdw = 1.2
vdwtype = Shift
; Electrostatics
coulombtype = Shift
any idea what is going on? am i seeing the water freeze @300K? anyone else experience something like this? thank you for any help.
i have a ~40 residue protein that i am trying to simulate with MARTINI. i ran a 100ns simulation that had previously worked on a ~140 residue protein. at about 3ns the potential energy plummets, rmsd becomes nearly a flat line. i'm using a dt of 20fs and the non-polarizable water. here is my .mdp:
; Run parameters
integrator = md
nsteps = 5000000
dt = 0.02
tinit = 0
nstcomm = 1
comm_mode = linear
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstxtcout = 1000
xtc_precision = 1000
nstenergy = 1000
; Bond parameters
constraints = none
constraint_algorithm = lincs
lincs_order = 4
lincs_warnangle = 30
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.4
rcoulomb = 1.2
epsilon_r = 15
rvdw = 1.2
vdwtype = Shift
; Electrostatics
coulombtype = Shift
any idea what is going on? am i seeing the water freeze @300K? anyone else experience something like this? thank you for any help.
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- xavier
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13 years 2 months ago #564
by xavier
Freezing might occur at 300K if you have one of these conditions:
-small solvatation box
-interface that increases the structure of water
-an even small nucleus of structured water
You can avoid freezing by adding 10% of antifreeze particles.
Replied by xavier on topic Strange behaviour @ ~3ns for ~40 residue protein
It might be that your water is freezing. Did you visualize the trajectory? If freezing occurs it will appear clearly.johnny wrote: hello,
i have a ~40 residue protein that i am trying to simulate with MARTINI. i ran a 100ns simulation that had previously worked on a ~140 residue protein. at about 3ns the potential energy plummets, rmsd becomes nearly a flat line. i'm using a dt of 20fs and the non-polarizable water. here is my .mdp:
; Run parameters
integrator = md
nsteps = 5000000
dt = 0.02
tinit = 0
nstcomm = 1
comm_mode = linear
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstxtcout = 1000
xtc_precision = 1000
nstenergy = 1000
; Bond parameters
constraints = none
constraint_algorithm = lincs
lincs_order = 4
lincs_warnangle = 30
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.4
rcoulomb = 1.2
epsilon_r = 15
rvdw = 1.2
vdwtype = Shift
; Electrostatics
coulombtype = Shift
any idea what is going on? am i seeing the water freeze @300K? anyone else experience something like this? thank you for any help.
Freezing might occur at 300K if you have one of these conditions:
-small solvatation box
-interface that increases the structure of water
-an even small nucleus of structured water
You can avoid freezing by adding 10% of antifreeze particles.
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- johnny
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13 years 2 months ago #587
by johnny
Replied by johnny on topic Strange behaviour @ ~3ns for ~40 residue protein
thanks for the reply. i am trying to visualize the trajectory, but am having trouble getting vmd to display correctly. i will try the antifreeze particles as well. it is also a small-ish dodeca "box" so that may also be an issue. what do you suggest for visualizing MARTINI trajectories?
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- xavier
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13 years 2 months ago #590
by xavier
VMD is fine. Using dynamic bonds is useful some times.
Replied by xavier on topic Strange behaviour @ ~3ns for ~40 residue protein
johnny wrote: thanks for the reply. i am trying to visualize the trajectory, but am having trouble getting vmd to display correctly. i will try the antifreeze particles as well. it is also a small-ish dodeca "box" so that may also be an issue. what do you suggest for visualizing MARTINI trajectories?
VMD is fine. Using dynamic bonds is useful some times.
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- johnny
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13 years 2 months ago #594
by johnny
Replied by johnny on topic Strange behaviour @ ~3ns for ~40 residue protein
got it. will try. thanks for the very quick replies...
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