From: [EMAIL PROTECTED] <[EMAIL PROTECTED]>
Subject: gmx-users Digest, Vol 55, Issue 147
To: gmx-users@gromacs.org
Date: Friday, November 28, 2008, 3:59 PM
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Today's Topics:
1. Re: defination of cluster (Mark Abraham)
2. Box vector shifts number in x and y/z dimension
(xuji)
3. How to calculate virial in gromacs-4.0? (xuji)
4. RE: PME-user for electrostatics (Berk Hess)
5. Fatal error with grompp(with detail process) (Jenny
Hsu)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Nov 2008 12:24:52 +1100
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] defination of cluster
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Q. Y. HUAN wrote:
Dear all,
I did the g_clustsize to get the number of cluster
graph for my system. At the end of the simulation, the total
number of cluster shown in the graph of my system was 8.
Then I had a view in the trjectory and I found that there
were total of 8 aggregated micelles and some free monomer
(even it is a single molecule) which is same with the result
shown in the graph.
ie 8 in the graph, 8 in the trajectory
My question is, how Gromacs define the defination of
cluster? In my case, is it a free monomer (single free
molecule) is also counted?
Did you start by reading g_clustsize -h?
Mark
------------------------------
Message: 2
Date: Fri, 28 Nov 2008 09:41:31 +0800
From: "xuji"<[EMAIL PROTECTED]>
Subject: [gmx-users] Box vector shifts number in x and y/z
dimension
To: "gmx-users@gromacs.org"
<gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="gb2312"
Hi all:
In gromacs all atoms are in the rectangular or triclinic
unit-cell,
and in the codes using shifts with periodic boundary
condition.
But why are there only single box vector shifts required in
y and z dimensions
but 2 in x dimension ?
Thanks for any help in advance!
xuji
[EMAIL PROTECTED]
2008-11-28
------------------------------
Message: 3
Date: Fri, 28 Nov 2008 15:32:55 +0800
From: "xuji"<[EMAIL PROTECTED]>
Subject: [gmx-users] How to calculate virial in
gromacs-4.0?
To: "gmx-users@gromacs.org"
<gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="gb2312"
Hi all
I want to do pressure coupling in my own program.
So These days I read associated codes in Gromacs_4.0 and I
find that it
must sum the virial first. In Gromacs-3.3.3 you use the
intramolecular shift(graph)
to sum the virial of the covalent bonds, but in Gromacs-4.0
the graph variable seems to be NULL
when run the mdrun with domain decomposition. Is it the
true?
And if it's true how do you sum the virial with the
periodic boundary condition
in Gromacs_4.0 with domain decomposition? Can someone
explain the way of summing
virial in Gromacs_4.0 in detail? Or can you recommend some
resoures about summing the virial with
the periodic boundary condition?
Appreciate any help in advance!
Best
wishes!
xuji
[EMAIL PROTECTED]
2008-11-28
------------------------------
Message: 4
Date: Fri, 28 Nov 2008 08:56:16 +0100
From: Berk Hess <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] PME-user for electrostatics
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
PME splits the calculation in a Mesh part and a direct
space part,
which is normally 1/r minus the mesh part. Note that the
mesh part
also contributes below the cut-off.
If you want something else than 1/r at short range
(you always have 1/r beyond the cut-off)
than you can just give the short-range potential you want,
mdrun takes care that it subtracts the short range
contribution of the mesh part.
Berk
Date: Thu, 27 Nov 2008 13:37:36 -0800
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] PME-user for electrostatics
hi,
i want to use a different function than the Coulomb to
calculate the electrostatics
between charged ions. So i am thinking to user the
PME-user option for the electrostatics.
The manual says for the PME-user option"The PME
mesh contribution is subtracted from the user table by
mdrun".
what that means? should i have to add the
short-range-potential (given by equation-4.33 in the manual)
in the user table, because that will be subtracted
with the mdrun?
please let me know, and thanks a lot for your help
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Message: 5
Date: Fri, 28 Nov 2008 15:58:41 +0800
From: "Jenny Hsu" <[EMAIL PROTECTED]>
Subject: [gmx-users] Fatal error with grompp(with detail
process)
To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi all:
I have a problem with grompp
I want to making "POPC+protein" file
and I search the archieve and follow the process
1.run pdb2gmx for protein only
2.add below parameters into my topology file
#include "ffG53a6.itp"
#include "lipid.itp"
#include "popc.itp"
3.adjust the [ molecules ] section to list the number and
type of my
components
4.run editconf and genbox
5.run grompp and it shows
Fatal error:
Atomtype CA not found
*Below is all information it shows*
*Can someone help me to solve this problem?*
*I am appreciate with that.*
*Thaks.*
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in
Calculating Stuff
:-) VERSION 4.0 (-:
Written by David van der Spoel, Erik Lindahl, Berk
Hess, and others.
Copyright (c) 1991-2000, University of Groningen,
The Netherlands.
Copyright (c) 2001-2008, The GROMACS
development team,
check out http://www.gromacs.org for more
information.
This program is free software; you can
redistribute it and/or
modify it under the terms of the GNU General
Public License
as published by the Free Software Foundation;
either version 2
of the License, or (at your option) any later
version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file with MD
parameters
-po mdout.mdp Output grompp input file with MD
parameters
-c 1UEO-nowater_water.gro Input Structure file:
gro g96 pdb tpr
tpb
tpa
-r conf.gro Input, Opt. Structure file: gro g96
pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96
pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 1UEO-nowater.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 1UEO-nowater_em.tpr Output Run input file: tpr
tpb tpa
-t traj.trr Input, Opt. Full precision
trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after
this time.
-[no]rmvsbds bool yes Remove constant bonded
interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings
during input
processing
-[no]zero bool no Set parameters for bonded
interactions without
defaults to zero instead of
generating an error
-[no]renum bool yes Renumber atomtypes and minimize
number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6.itp
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6nb.itp
Opening library file
/usr/local/md/share/gromacs/top/ffG53a6bon.itp
Opening library file
/usr/local/md/share/gromacs/top/ff_dum.itp
WARNING 1 [file lipid.itp, line 14]:
Overriding atomtype LO
WARNING 2 [file lipid.itp, line 15]:
Overriding atomtype LOM
WARNING 3 [file lipid.itp, line 16]:
Overriding atomtype LNL
WARNING 4 [file lipid.itp, line 17]:
Overriding atomtype LC
WARNING 5 [file lipid.itp, line 18]:
Overriding atomtype LH1
WARNING 6 [file lipid.itp, line 19]:
Overriding atomtype LH2
WARNING 7 [file lipid.itp, line 20]:
Overriding atomtype LP
WARNING 8 [file lipid.itp, line 21]:
Overriding atomtype LOS
WARNING 9 [file lipid.itp, line 22]:
Overriding atomtype LP2
WARNING 10 [file lipid.itp, line 23]:
Overriding atomtype LP3
WARNING 11 [file lipid.itp, line 24]:
Overriding atomtype LC3
WARNING 12 [file lipid.itp, line 25]:
Overriding atomtype LC2
WARNING 13 [file lipid.itp, line 108]:
Overriding non-bonded parameters,
old: 0.00238804 3.38411e-06 new
LNL C 1 2.387718e-03 2.389594e-06
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 793
Fatal error:
Atomtype CA not found
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
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