[gmx-users] how to start simulation of a peptide in bilayer
nur avneet
nuravneet at yahoo.co.in
Wed Nov 1 10:27:16 CET 2006
I am new to gromacs and need guidance to start a simulation of a peptide in bilayer.
Please guide
gmx-users-request at gromacs.org wrote: Send gmx-users mailing list submissions to
gmx-users at gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-request at gromacs.org
You can reach the person managing the list at
gmx-users-owner at gromacs.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. Re: indexing atoms (Erik Marklund)
2. rdf (Claus Valka)
3. potential oxiredution (Elias santos)
4. Re: potential oxiredution (Mark Abraham)
5. Re: problem in compiling g_velacc again under gromacs
(Mark Abraham)
6. Re: problem in compiling g_velacc again under gromacs (Qiao Baofu)
7. Re: problem in compiling g_velacc again under gromacs (Qiao Baofu)
8. pulldim vectors in pull code (Mauricio Sica)
----------------------------------------------------------------------
Message: 1
Date: Tue, 31 Oct 2006 09:39:01 +0100
From: Erik Marklund
Subject: Re: [gmx-users] indexing atoms
To: Discussion list for GROMACS users
Message-ID: <1162283942.28794.6.camel at jorn.bmc.uu.se>
Content-Type: text/plain; charset=utf-8
You can sort the atoms according to position using grompp, but I don't
think that's the easiest solution. I would use awk or something along
those lines, to find all atoms within z=[4 5] nm and remove everything
except the indexes. Put a bracketed name on top of it all and violà , you
have turned them into an index group.
/Erik
On Tue, 2006-10-31 at 00:37 -0600, toma0052 wrote:
> Hello,
> I have a question regarding indexing atoms for use with
> non-equilibrium MD. The manual says that I can select atoms by number or
> type; I was wondering if there is a way in Gromacs to index atoms by
> position with the simulation box. I am looking to add an acceleration to
> the solvent, but not the entire solvent. Is there a way that I can specify
> solvent molecules within a certain coordinate ie. a z-position from 4nm to
> 5nm with the simulation box being 6nm in height? I am looking to
> accelerate solvent molecules near a lipid bilayer, but if a particular
> solvent molecule diffuses too far from the bilayer, I no longer want it to
> keep its fixed acceleration. Is there any way that indexing by coordinates
> is possible?
>
> Thank you,
> Mike Tomasini
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se
------------------------------
Message: 2
Date: Tue, 31 Oct 2006 13:16:27 +0100 (CET)
From: Claus Valka
Subject: [gmx-users] rdf
To: gmx-users at gromacs.org
Message-ID: <20061031121627.71473.qmail at web26602.mail.ukl.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Title : radial distribution function, 31.10.06
Hello,
I am a new user of Gromacs (just started my
Phd), and
I'm trying to calculate the partial radial
distibution functions
for a system of polymer chains.
In the topology file the system is described as
1) 2 different types of chains
(essentially similar in chemistry, with
different helicity)
2) C, H, CH3 atom types in each chain (3
different bead types)
I would like to calculate the rdfs for the
partial correlations
corresponding to pairs of the type
a) C - all
b) C - C
c) C - CH3
d) C - H
e) CH3 - H
for
A) intra-pairs (same chain)
B) inter-pairs (different chains)
C) any pair
i.e., pair correlations A[a,b,c,d,e], B[...] and
so on,
over all chains in the system.
In the manual it is said that an index file is
needed
How could I describe the groups in index file so
as to make these
calculations in an efficient way? Is there any
easy way to describe
various kind of desired 'pairing correlations'
in Gromacs?
Any help would be appreciated,
Nick
___________________________________________________________
Telefonate ohne weitere Kosten vom PC zum PC: http://messenger.yahoo.de
------------------------------
Message: 3
Date: Tue, 31 Oct 2006 10:56:29 -0200
From: "Elias santos"
Subject: [gmx-users] potential oxiredution
To: gmx-users
Message-ID:
<97baf6380610310456v6378b0dfj15ea88bdcef038fa at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi!!
I have a question for you...
Some way to calculate the oxiredution potential (ORP) using the Gromacs
package?
Elias
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20061031/fef95973/attachment-0001.html
------------------------------
Message: 4
Date: Wed, 01 Nov 2006 00:10:34 +1100
From: Mark Abraham
Subject: Re: [gmx-users] potential oxiredution
To: Discussion list for GROMACS users
Message-ID: <45474B4A.6080206 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Elias santos wrote:
> Some way to calculate the oxiredution potential (ORP) using the Gromacs
> package?
No, since you can't simulate a system with MD that's large enough that
such a bulk observable would be at all meaningful - and even then you'd
get out the answer you put in by choosing the solutes.
Mark
------------------------------
Message: 5
Date: Wed, 01 Nov 2006 00:19:05 +1100
From: Mark Abraham
Subject: Re: [gmx-users] problem in compiling g_velacc again under
gromacs
To: Discussion list for GROMACS users
Message-ID: <45474D49.9000907 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Qiao Baofu wrote:
> Hi all,
>
> I want to comile the g_velacc again. I copy the original gmx_velacc.c
> and autocorr.c into a new directory, and then comile the gmx_velacc.c,
> but it gives the following complains, and then exits. (I didn't change
> anything in the two files!!) How to solve it? Thanks a lot.
Does it work if you do it in the same directory? That's got to be cleaner...
Mark
------------------------------
Message: 6
Date: Tue, 31 Oct 2006 15:07:26 +0100
From: "Qiao Baofu"
Subject: Re: [gmx-users] problem in compiling g_velacc again under
gromacs
To: "Discussion list for GROMACS users"
Message-ID:
<6a91f07b0610310607r1c6b6c93lc042a1f04df1e736 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I compile it again in the source folder ~/src/tool/ and the installation
folder ~/gromacs/bin. It give the same complains.
What can I do?
2006/10/31, Mark Abraham :
>
> Qiao Baofu wrote:
> > Hi all,
> >
> > I want to comile the g_velacc again. I copy the original gmx_velacc.c
> > and autocorr.c into a new directory, and then comile the gmx_velacc.c,
> > but it gives the following complains, and then exits. (I didn't change
> > anything in the two files!!) How to solve it? Thanks a lot.
>
> Does it work if you do it in the same directory? That's got to be
> cleaner...
>
> Mark
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20061031/472f21b5/attachment-0001.html
------------------------------
Message: 7
Date: Tue, 31 Oct 2006 16:19:14 +0100
From: "Qiao Baofu"
Subject: Re: [gmx-users] problem in compiling g_velacc again under
gromacs
To: "Discussion list for GROMACS users"
Message-ID:
<6a91f07b0610310719ne37ed8x5684ea3327cc2426 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
I think the problem is because I compile Gromacs under 64-bite model. the
g_velacc.c can not be recognized under 64 bite model.
But when I compile it under 32-bite it gives the following complains. On the
other hand I am not sure whether a file (which is ok under 32-bite system )
can be copied to 64-bite system.
/usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when
searching for -lmd
/usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when
searching for -lmd
/usr/bin/ld: cannot find -lmd
collect2: ld returned 1 exit status
2006/10/31, Qiao Baofu :
>
> Hi,
>
> I compile it again in the source folder ~/src/tool/ and the installation
> folder ~/gromacs/bin. It give the same complains.
>
> What can I do?
>
>
> 2006/10/31, Mark Abraham < Mark.Abraham at anu.edu.au>:
> >
> > Qiao Baofu wrote:
> > > Hi all,
> > >
> > > I want to comile the g_velacc again. I copy the original gmx_velacc.c
> > > and autocorr.c into a new directory, and then comile the gmx_velacc.c,
> > > but it gives the following complains, and then exits. (I didn't change
> >
> > > anything in the two files!!) How to solve it? Thanks a lot.
> >
> > Does it work if you do it in the same directory? That's got to be
> > cleaner...
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Sincerely yours,
> **********************************************
> Baofu Qiao, PhD
> Frankfurt Institute for Advanced Studies
> Max-von-Laue-Str. 1
> 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
> **********************************************
>
--
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20061031/0c495e5d/attachment-0001.html
------------------------------
Message: 8
Date: Tue, 31 Oct 2006 17:21:57 -0300
From: "Mauricio Sica"
Subject: [gmx-users] pulldim vectors in pull code
To:
Message-ID: <003d01c6fd2a$3f3b9140$3800020a at CYT032>
Content-Type: text/plain; charset="iso-8859-1"
Dear users
I have the following problem. I'm using the pull code to bring near two
peptides initially 2.7 nm apart. The problem is that the run crush when I
choose "pulldim = Y Y Y or Y N N ", but doesn't when I use N N Y. I can't
understand what's wrong.
Maybe I don't understand what's the vector I am choosing in pulldim option.
I know it is the x, y or z axis. But is it a box vector? A distance vector?
In this case, why x, y and z if distance is one-dimensional? It was not
clear (at least for me) in the manuals (3.2 or
3.3)
Thanks in advance
My pull.ppa is
---------------
verbose = no
Skip steps = 10
runtype = constraint
ngroups = 1
group_1 = G1
reference_group = GR
reftype = com_t0
reflag = 1
pulldim = Y Y Y or N N Y or Y N N ; the three options I used. Only N N Y
worked
constraint_direction = 0.0 0.0 0.0
constraint_distance1 =
constraint_rate1 = -0.00007
constraint_tolerance = 0.1
Dr. Mauricio Pablo Sica
Laboratorio de Expresión y Plegado Proteico (LEPP)
Dpto. de Ciencia y Tecnología
Universidad Nacional de Quilmes (UNQ)
R. Saenz Peña 352 (B1876BXF)
Bernal, Pcia de Buenos Aires
Argentina
------------------------------
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
End of gmx-users Digest, Vol 30, Issue 75
*****************************************
---------------------------------
Find out what India is talking about on - Yahoo! Answers India
Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20061101/fe3c9389/attachment.html>
More information about the gromacs.org_gmx-users
mailing list