Dear Axel,
I changed the input script as below:
group pull id 409
group surf molecule 1
fix 3 pull move linear NULL NULL 0.0001 units box
fix 2 surf spring/self 100.0 z
compute 1 pull group/group surf
fix 1 all nvt temp 298.15 298.15 100.0
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp
evdwl ecoul elong press c_1[3] c_2[3] c_3 c_3[1] c_3[2] c_3[3]
I just want to make sure that whatever force is added to the system does not
have any contribution to the amount of force calculated by the compute
command (btw atom 409 & surface).
i don't think that this will work correctly.
a) you need to exclude the group pull from the nvt thermostat,
right now it is integrated twice.
b) you are not really following the requirements for steered md,
since you have now an "infinitely hard" spring. you'll be pulling
that one atom at absolutely constant velocity, that is true, but
i would worry what kind of result you can extract from that.
axel.
Well yes you are right about the stiff spring
How can I change the stiffness of the spring along the path (to make it larger close to the surface and smaller when it is off of the surfaces?) I tries fix smd but atoms comes off of the surface and then jumps to the middle of the box, not letting those areas to be sampled
does the * fix 2 surf spring/self 100.0 z* integrate the surf atoms too? so I have to exclude both atom 409 &surf from the thermostat, is that right?
I am running the umbrella sampling as well, and would like to see how two methods compare (since smd can be done mush faster)
Thanks again
Well yes you are right about the stiff spring
How can I change the stiffness of the spring along the path (to make it
larger close to the surface and smaller when it is off of the surfaces?) I
that doesn't make sense. please have a closer look at
the methodology and statistical mechanical justification
of why steered MD gives you a free energy.
tries fix smd but atoms comes off of the surface and then jumps to the
middle of the box, not letting those areas to be sampled
that is likely not the fault of fix smd, but has to be due to your setup.
it could be that you are pulling too fast or that your surface is not
properly set up. this is near impossible to judge from the little
information that you are providing.
does the * fix 2 surf spring/self 100.0 z* integrate the surf atoms too?
no. those things are explained *in detail* in the documentation.
please don't abuse the mailing list as a replacement for
becoming familiar with the documentation. this just
irritates people (and particularly me). thanks.
so I have to exclude both atom 409 &surf from the thermostat, is that right?
depends.
I am running the umbrella sampling as well, and would like to see how two
methods compare (since smd can be done mush faster)
you apparently have not looked at how steered MD works.
for a simple reaction coordinate, umbrella sampling always
wins, since you can choose when a bin is converged and
you can easily parallelize the calculation in an embarrassing
way. steered MD requires almost always multiple runs to
result in equally well converged free energy profiles.
this is why the documentation to fix smd has references.
those describe the method and also discuss errors and
proper usage (including choice of steering velocity
and force constant).
axel.