priyanka srivastava wrote:
Hie,
Many thanks for your reply.
Yes I have used semi-isotropic coupling.
Another doubt is why only a value of 4.5e-5?
I have used PME and have mentioned rcoulomb in the
.mdp file too, which as is pointed out by you, has no
meaning!! But does this mean that my mdp file is
wrong? Because if PME does not use rcoulomb it shud
simply ignore the value.
Actually I do not want to use twin range cutoff. So, I
have given rvdw = rlist. Is this alright?
Portion of my mdp file looks like this:
; Electrostatics
coulombtype = PME
fourier_nx = 6.4
fourier_ny = 5.0
fourier_nz = 8.1
these numbers should be integers
pme_order = 4
rcoulomb = 1.5
rvdw = 1.5
Also since I have not specified "vdwtype" in the mdp
file, so it automatically takes Cut-off.
regards,
Pri...
--- Martin Höfling <[EMAIL PROTECTED]> wrote:
Am Mittwoch, 20. Juni 2007 schrieb priyanka
srivastava:
I am currently involved in doing a lipid-peptide
simulation under NPAT conditions. The way I have
applied NPAT condition is as follows:
ref_p = 0 1
compressibility = 0.0 4.5e-5
with semiisotropic?
Although while performing analysis it shows that
the x
and y dimensions are constant but still I am not
sure
about the way I have applied NPAT. Could somone
please
tell me the basis behind it?
If i am remembering correctly, this is what above
values should do:
first dimension is x-y second one is the z
direction. Reference pressure is 1
for both (obviously makes sense) whereas
compressibility set to 0 for x-y
plane prevents box changes in x and y direction. So
only z-direction remains
for adjusting pressure.
Another thing is I have used vdwtype: cutoff.
But my intention is not to use the twin range
cutoff
at all!! In my case rlist = rcoulomb = rvdw, i.e.
all
three are same!! Is this alright? (the coulombtype
= PME)
Sorry, didn't get that part of your question. Can
you post relevant parts of
your mdp and specify it further? Chapter 7 says that
parameters for PME are
fourierspacing and pme_order, rcoulomb should not be
used then.
Cheers
Martin
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