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Today's Topics:
1. Surface Tension of a lipid bilayer (toma0052)
2. opls parameters (Komath Damodaran)
3. Segmentaion fault error- installing gromacs-3.3.1 on MacOSX
(Ibrahim M. Moustafa)
4. Question about NVT (Justin Lemkul)
5. References for globular protein simulation using PME (Dilraj Lama)
6. Re: Surface Tension of a lipid bilayer (David van der Spoel)
7. Re: Segmentaion fault error- installing gromacs-3.3.1 on
MacOSX (David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Fri, 01 Dec 2006 16:59:20 CST
From: toma0052 <[EMAIL PROTECTED]>
Subject: [gmx-users] Surface Tension of a lipid bilayer
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: TEXT/plain; CHARSET=US-ASCII
Hello,
I have a question about calculating the surface tension for the
water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr
file and g_energy to calculate the surface tension. I believe that the
surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L. I
was wondering though, is the pressure tensor and hence surface tension
calculated over the entire simulation box? I would assume so, since I did
not specify any molecules. To find the water-lipid surface tension, would I
not need to sum over only the molecules at the surface? Would this be
do-able in Gromacs? Would I have to write something separate to do this?
In my coordinate file, I have DPPC atoms, solvent atoms, and other atoms
(those that make up the head group ie O,N etc.). Could I just make an index
group that is not DPPC and not Solvent, and sum over those atoms?
Thanks,
Mike Tomasini
------------------------------
Message: 2
Date: Fri, 1 Dec 2006 16:35:32 -0800
From: "Komath Damodaran" <[EMAIL PROTECTED]>
Subject: [gmx-users] opls parameters
To: <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
Hi All,
I am trying to build the itp file for a molecule. I would like to use
the opls force field. The ffoplsaa.atp contains the atom types as
opls_xxx. But the ffoplsbon.itp which contains the bond-angle-dihedral
parameters does not use the opls_xxx convention. Is there a way to
identify the bond/angle/torsion parameters of a set of opls_xxx atoms?
Thanks very much!
Dam
-------------------------------------------
Komath Damodaran
Scientist, Computational Chemistry
Telik, Inc.
3165 Porter Drive
Palo Alto, CA 94304
Tel: (650) 845-7838, Fax: 650-845-7800
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------------------------------
Message: 3
Date: Fri, 01 Dec 2006 21:15:18 -0500
From: "Ibrahim M. Moustafa" <[EMAIL PROTECTED]>
Subject: [gmx-users] Segmentaion fault error- installing gromacs-3.3.1
on MacOSX
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Hi gmx-users,
I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
After installation (either building the package myself as instructed,
or using a binary form GROMACS web site) I could not run any program
with just typing the name on the xterm!
for example, issuing "pdb2gmx" command line gives an error message
"segmentation fault". However, typing the whole path name
"$GMXBIN/pdb2gmx or any other modules " works fine.
The variables for GROMACS are configured after the installation. My
.cshrc sources from the GMXRC.csh and the variables are defined; the
PATH includes the $GMXBIN also.
For the moment, I'm using alias to define the whole path for GROMACS
programs to run; though, this a bit annoying.
I posted this problem in CCL and M.L. Dodson, replied with some
explanation for this weird problem:
" Ahh... Think I have it. Looking at the source code on my BSD Unix
box, I see in src/gmxlib/copyrite.c the following:
void CopyRight(FILE *out,char *szProgram)
{
/* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
* name of a file. Otherwise, we won't be able to find the library dir.
*/
#define NCR (int)asize(CopyrightText)
#define NGPL (int)asize(GPLText)
char buf[256],tmpstr[1024];
char *ptr;
int i;
set_program_name(szProgram);
.
.
.
So I was right, it does use argv[0] for something: finding its
library directory."
I wonder if there is a quick fix for this in the code, so I can
run the programs by just typing the name without need for the whole path!
A question here: if Dodson is right, why the programer wrote the
code this way! is there any advantage?
P.S. I have no previous experience with GROMACS
thanks,
Ibrahim
------------------------------
Message: 4
Date: Sat, 2 Dec 2006 00:07:48 -0500
From: Justin Lemkul <[EMAIL PROTECTED]>
Subject: [gmx-users] Question about NVT
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Hello all,
I have a quick question regarding an MD simulation I am attempting to run
(again, the membrane protein which I had problems with previously). Thanks to
the helpful suggestions; my system is now well-minimized! The last
step before
I would like to take before running full-out MD on my system is to equilibrate
my solvent and ions over a short timeframe (100ps). My initial attempts have
been unsuccessful; the equilibration proceeds nicely for 960 steps (1.920 ps)
before I get a screen full of LINCS warnings. Apparently one of my DPPC
molecules is being blown apart. I have placed position restraints on both my
protein and my bilayer, in order to allow the solvent and ions (Na+) to move
around them. I have attached my equil.mdp file below, in case I am making any
obvious mistakes. I am piecing my .mdp file together from several
examples and
tutorials.
My value for nstlog is set very small so I could monitor energies,
etc after the
first failure...in case anyone was wondering :)
Thanks in advance for your kind advice in helping out a newbie.
-Justin
PS - I'm running Gromacs v3.3 on Mac OSX v10.4.8, in case any of that matters.
----------
title = MD equilibration of solvent and ions
cpp = /usr/bin/cpp
include = -I./
define = -DPOSRES -DPOSRES_LIPID
integrator = md
nsteps = 50000
nstlist = 10
nstxout = 1000
nstvout = 1000
nstlog = 10
nstenergy = 1000
nstxtcout = 1000
dt = 0.002
ns_type = simple
coulombtype = cut-off
rlist = 0.9
rvdw = 0.9
rcoulomb = 0.9
fourierspacing = 0.12
; Temperature coupling is on in four groups
tcoupl = berendsen
tc_grps = Protein DPPC SOL NA+
tau_t = 0.1 0.1 0.1 0.1
ref_t = 323 323 323 323
; Pressure coupling is not on
Pcoupl = no
ref_p = 1.0
gen_vel = no
gen_temp = 323
constraints = all-bonds
constraint_algorithm = lincs
optimize_fft = yes
DispCorr = EnerPres
pbc = full
---------
Justin A. Lemkul
Department of Biochemistry
Virginia Tech
------------------------------
Message: 5
Date: Sat, 2 Dec 2006 13:37:55 +0530 (IST)
From: "Dilraj Lama" <[EMAIL PROTECTED]>
Subject: [gmx-users] References for globular protein simulation using
PME
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;charset=iso-8859-15
Dear all gmx-users,
I have been trying to dig out some well cited paper on
simulation of globular protein using PME .Can anyone
please suggest to me some references I can look out
for.
Thanks to all.
--
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973
------------------------------
Message: 6
Date: Sat, 02 Dec 2006 10:22:21 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Surface Tension of a lipid bilayer
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
toma0052 wrote:
> Hello,
> I have a question about calculating the surface tension for the
> water-lipid interface of a lipid bilayer. After an MD run, I can
use my .edr
> file and g_energy to calculate the surface tension. I believe that the
> surface tension is calculated something like gamma =
(Pzz-(Pxx+Pyy)/2)/L. I
> was wondering though, is the pressure tensor and hence surface tension
> calculated over the entire simulation box? I would assume so, since I did
> not specify any molecules. To find the water-lipid surface
tension, would I
> not need to sum over only the molecules at the surface? Would this be
> do-able in Gromacs? Would I have to write something separate to do this?
> In my coordinate file, I have DPPC atoms, solvent atoms, and
other atoms
> (those that make up the head group ie O,N etc.). Could I just
make an index
> group that is not DPPC and not Solvent, and sum over those atoms?
>
> Thanks,
> Mike Tomasini
First, one usually has two interfaces, in which case you have to divide
the surface tension by two. This is computed over the entire box but it
will give you a perfectly good result.
Further it would be interesting to calculate local pressures, and there
is an ancient gromacs version that does this (can be downloaded from the
website). The reason this is not in standard gromacs is that it is quite
expensive to compute.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 7
Date: Sat, 02 Dec 2006 10:25:03 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Segmentaion fault error- installing
gromacs-3.3.1 on MacOSX
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Ibrahim M. Moustafa wrote:
> Hi gmx-users,
>
> I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
> After installation (either building the package myself as instructed, or
> using a binary form GROMACS web site) I could not run any program with
> just typing the name on the xterm!
> for example, issuing "pdb2gmx" command line gives an error message
> "segmentation fault". However, typing the whole path name
> "$GMXBIN/pdb2gmx or any other modules " works fine.
> The variables for GROMACS are configured after the installation. My
> .cshrc sources from the GMXRC.csh and the variables are defined; the
> PATH includes the $GMXBIN also.
> For the moment, I'm using alias to define the whole path for GROMACS
> programs to run; though, this a bit annoying.
>
> I posted this problem in CCL and M.L. Dodson, replied with some
> explanation for this weird problem:
>
> " Ahh... Think I have it. Looking at the source code on my BSD Unix
> box, I see in src/gmxlib/copyrite.c the following:
>
> void CopyRight(FILE *out,char *szProgram)
> {
> /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
> * name of a file. Otherwise, we won't be able to find the library dir.
> */
> #define NCR (int)asize(CopyrightText)
> #define NGPL (int)asize(GPLText)
>
> char buf[256],tmpstr[1024];
>
> char *ptr;
>
> int i;
>
> set_program_name(szProgram);
> .
> .
> .
>
> So I was right, it does use argv[0] for something: finding its
> library directory."
>
> I wonder if there is a quick fix for this in the code, so I can run
> the programs by just typing the name without need for the whole path!
>
> A question here: if Dodson is right, why the programer wrote the code
> this way! is there any advantage?
>
> P.S. I have no previous experience with GROMACS
>
> thanks,
> Ibrahim
> _______________________________________________
> gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Have you tried
source $GMXBIN/GMXRC
It will set up the necessary environment variables after which you can
run it as usual (I do it all the time on my Macs).
The advantage with this code is that you should be able to move the
entire gromacs installation somewhere else.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
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