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Dear prof. Berk,<br>
<br>
Since it is the first time I use the tabulated potential, I have lots
of questions about it. Could you help me out? Thanks a lot!<br>
<br>
I make the test in the system with only some waters between 2 implicit
walls.<br>
1. some related parameters of the .mdp file are listed below. Is there
anything wrong? <br>
energygrps = SOL<br>
pbc = xy<br>
rlist = 1.2<br>
coulombtype = pme<br>
rcoulomb = 1.2<br>
vdw-type = cut-off<br>
rvdw = 1.2<br>
DispCorr = EnerPres<br>
table-extension = 1<br>
energygrp_table = <br>
;Walls<br>
nwall = 2<br>
wall_type = table <br>
wall_r_linpot = 0.0<br>
wall_atomtype = opls_135 opls_135 <br>
wall_density = ;<b>(the wall_density is included in
the tabulated potential, right?)</b> <br>
wall_ewald_zfac = 3<br>
<br>
2. The flags of mdrun are:<br>
mdrun -deffnm table -tablep table_SOL_wall0.xvg
table_SOL_wall1.xvg -table table.xvg<br>
where table.xvg is copied from gmx_top_path/table6-12.xvg, and
table_SOL_wall0.xvg and table_SOL_wall1.xvg are the self-generated 9-3
potential (9-3 potential is used for the aim of testing and compare
with the default 9-3 potential of gromacs.)<br>
<b>Since I use only the tabulated potential between SOL-wall0 and
SOL-wall1, why do I need the table.xvg? Does it affect the coulomb/vdw
potential between SOL-SOL?</b><br>
<br>
3. In the table_SOL_wall0.xvg and table_SOL_wall1.xvg, the distance
range of 0-3nm is generated. max(rvdw, rcoulomb)=1.2 nm and
table-extension=1. The question is <b>what is the cutoff distance for
the tabulated SOL-wall0/wall1 potential, 2.2nm or 3nm?<br>
</b><br>
4. In the output file table.log,<br>
Table routines are used for coulomb: TRUE<br>
Table routines are used for vdw: FALSE<br>
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald<br>
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2<br>
System total charge: 0.000<br>
Generated table with 1100 data points for Ewald.<br>
Tabscale = 500 points/nm<br>
Generated table with 1100 data points for LJ6.<br>
Tabscale = 500 points/nm<br>
Generated table with 1100 data points for LJ12.<br>
Tabscale = 500 points/nm<br>
Reading user tables for 1 energy groups with 2 walls<br>
Read user tables from table_SOL_wall0.xvg with 1501 data points.<br>
Tabscale = 500 points/nm<br>
Read user tables from table_SOL_wall1.xvg with 1501 data points.<br>
Tabscale = 500 points/nm<br>
<br>
The question are: <br>
<b>a) Since Table is not used for vdw (FALSE), why table is generated
for LJ6/LJ12?<br>
b) Where does the value of "1100" data points come from? (Since
rvdw=1.2, tabscale=500, it should be 1400, not 1100!?)<br>
c) 1501 data points is generated for table_SOL_wall0/wall1, the answer
of the 3rd question (cutoff value for the tabulated potential
calculation) should be 3nm, right?</b><br>
<br>
Sorry for the lots of questions!<br>
<br>
best wishes,<br>
Baofu Qiao<br>
<br>
Berk Hess wrote:
<blockquote cite="mid:COL113-W50CFE1384778B1A8A7A6908E730@phx.gbl"
type="cite">
<pre wrap="">Hi,
Why not use the tabulated wall potential?
That does not require are changes to the code.
Berk
</pre>
<blockquote type="cite">
<pre wrap="">Date: Tue, 5 Jan 2010 14:13:30 +0100
From: <a class="moz-txt-link-abbreviated" href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
Subject: [gmx-users] 10-4-3 implicit wall potential
HI all,
Does anyone have experience to implement the 10-4-3 implicit wall
potential? If I want to use it, which files do I need to change, except
wall.c? Can anyone give some suggestions?
Thanks a lot!
best wishes,
Baofu Qiao
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</blockquote>
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