Zhe Wu wrote:
Dear David,
Thank you so much for your reply! I did try to use nstlist = -1 and I
still cannot solve the energy drifting problem. And you can see my
problem in more detail from the following link:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047299.html
And you mentioned I should use shifted VDW. But in the way I use
tabulated potential, the option in vdwtype should be User so that I
can indicate I am using a lookup table for the tabulated potential.
(In my test case, I used the table provide by GMX 4.0.5
/share/gromacs/top/table6-12.xvg directly, and just changed its name
to be table.xvg.) So it seems to me there is no explicit way I can use
shift function. Or should I shift the function by changing the
potential in the table?
Yes you can make a shifted vdw table as well. A simple way to do this is
to select vdwtype = shift with the cutoffs of your choice and then run 1
step of MD with the -debug 1 option. Then the tables will be printed
into xvg files.
Thanks again for your help.
Zhe
On Tue, Dec 8, 2009 at 1:38 PM, David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
Zhe Wu wrote:
I agree with that. But I don't know why, when using tabulated
potential, I cannot even get a box of LJ particles to have energy
conservation in NVE. Anyone has some idea?
do you use shifted VdW and nstlist = 1 or nstlist = -1?
Zhe
On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole <x.peri...@rug.nl> wrote:
One solution would be to use tabulated potential for which the
analytical form does not matter.
On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote:
hong bingbing wrote:
Dear all,
Has anyone tried to use 2 van de Waals interaction types in one system?
For example, the system includes two components A and B. The van de
Waas
interaction for A is LJ type, while for B Buckingham form is used. Can
GROMACS support two forms simultaneously?
No. How would you describe the vdW interaction between an atom from A
and
one from B?
If the reason for this question is based on a desire to mix two force
fields - don't.
Mark
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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel
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