fix smd-free energy

Dear Lammps users,
I am using the streered MD applying fix smd to get the PMF of a peptide bound to the surface. Here are the commands I added into my input script,

group pep molecule 2 #peptide
group surf molecule 0 #surface
fix 1 all nvt temp 298.15 298.15 100.0
fix 2 pep smd cvel 20.0 -0.00015 tether NULL NULL 50.0 0.0
fix 3 surf spring/self 10.0
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press pxx pyy pzz f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7]

The f_z and pmf (versus simulation time-as the peptide detaches from the surface) are attached to this email

Although the pmf plot sound reasonable, I don’t understand the force plot. I thought the force should be higher once the peptide is on the surface (the beginning of the simulation) since the delR is at its max and hence F=-k deR^2 should be the highest. Could you please make a comment on this? (I really thank you)

Another question is that, if we are using "fix smd* in the cvel mod (as I used) then what is the spring constant, I mean if we want to get a constant velocity then the force should be calculated in order to give us the desired del x and hence the velocity. Why then we should specify a spring constant?

Regards
Arshia

pmf.wmf (45.1 KB)

pmf2.wmf (43.4 KB)

Dear Lammps users,
I am using the streered MD applying *fix smd* to get the PMF of a peptide
bound to the surface. Here are the commands I added into my input script,

group pep molecule 2 #peptide
group surf molecule 0 #surface
fix 1 all nvt temp 298.15 298.15 100.0
fix 2 pep smd cvel 20.0 -0.00015 tether NULL NULL 50.0
0.0
fix 3 surf spring/self 10.0
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp
evdwl ecoul elong press pxx pyy pzz f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]
f_2[6] f_2[7]

The f_z and pmf (versus simulation time-as the peptide detaches from the
surface) are attached to this email

Although the pmf plot sound reasonable, I don't understand the force plot. I
thought the force should be higher once the peptide is on the surface (the
beginning of the simulation) since the delR is at its max and hence F=-k
deR^2 should be the highest. Could you please make a comment on this? (I
really thank you)

Another question is that, if we are using "fix smd* in the cvel mod (as I
used) then what is the spring constant, I mean if we want to get a constant
velocity then the force should be calculated in order to give us the desired
del x and hence the velocity. Why then we should specify a spring constant?

you need it. i suggest that before continuing, you read about why
SMD works and what its sources of errors are and how you pick
the correct parameters. the papers quoted in the fix smd documentation
are a very good start. reading up on jarzynski equality and fluctuation
theorem doesn't hurt either, and while you're at it, check out umbrella
sampling.

also, you should really use couple mode and not tether plus fix spring self.

axel.